This unresolved issue might give some points that help move things along for you: https://github.com/zaproxy/zaproxy/issues/1602
Wish I could provide more but I don't have a place to test an ntlm example.
Thanks for pointing out the VMs, unfortunately I don't need client VMs I'd need an IIS and AD server VM to recreate the server scenario and test ZAP against it.
2017-04-20 18:36:01,540 [ZAP-ActiveScanner-0] INFO User - Authenticating user: domain\username2017-04-20 18:36:01,540 [ZAP-ActiveScanner-0] DEBUG DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.02017-04-20 18:36:01,540 [ZAP-ActiveScanner-0] DEBUG DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.12017-04-20 18:36:01,540 [ZAP-ActiveScanner-0] DEBUG DefaultHttpParams - Set parameter http.protocol.cookie-policy = compatibility2017-04-20 18:36:01,540 [ZAP-ActiveScanner-0] DEBUG MultiThreadedHttpConnectionManager - HttpConnectionManager.getConnection: config = HostConfiguration[host=http://webapp], timeout = 02017-04-20 18:36:01,540 [ZAP-ActiveScanner-0] DEBUG MultiThreadedHttpConnectionManager - Getting free connection, hostConfig=HostConfiguration[host=http://webapp]2017-04-20 18:36:01,541 [ZAP-ActiveScanner-0] DEBUG HttpMethodDirector - User defined 'Authorization' headers present in the request.2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "GET /About HTTP/1.1[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG HttpMethodBase - Adding Host request header2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Accept: application/x-ms-application, image/jpeg, application/xaml+xml, image/gif, image/pjpeg, application/x-ms-xbap, application/vnd.ms-excel, application/vnd.ms-powerpoint, application/msword, */*[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Referer: http://webapp/[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Accept-Language: en-US[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "User-Agent: Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.1; WOW64; Trident/7.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; .NET4.0E)[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Cookie: __AntiXsrfToken=cc5491bd15834e00838fe8f5d7823edc[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Proxy-Connection: Keep-Alive[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Authorization: Negotiate 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[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Content-Length: 0[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "Host: webapp[\r][\n]"2017-04-20 18:36:01,542 [ZAP-ActiveScanner-0] DEBUG header - >> "[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "HTTP/1.1 401 Unauthorized[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "Content-Type: text/html[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "Server: Microsoft-IIS/8.5[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "WWW-Authenticate: Negotiate[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "WWW-Authenticate: NTLM[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "X-Powered-By: ASP.NET[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "Date: Thu, 20 Apr 2017 22:36:01 GMT[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "Content-Length: 1293[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG header - << "[\r][\n]"2017-04-20 18:36:01,544 [ZAP-ActiveScanner-0] DEBUG HttpMethodDirector - Authorization required2017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] DEBUG AuthChallengeProcessor - Supported authentication schemes in the order of preference: [ntlm, digest, basic, ntlm]2017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] INFO AuthChallengeProcessor - ntlm authentication scheme selected2017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] DEBUG AuthChallengeProcessor - Using authentication scheme: ntlm2017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] DEBUG AuthChallengeProcessor - Authorization challenge processed2017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] DEBUG HttpMethodDirector - Authentication scope: NTLM <any realm>@webapp:802017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] DEBUG HttpMethodDirector - Credentials required2017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] DEBUG HttpMethodDirector - Credentials provider not available2017-04-20 18:36:01,545 [ZAP-ActiveScanner-0] INFO HttpMethodDirector - No credentials available for NTLM <any realm>@webapp:80No indicators have been set for identifying authentication. Assuming response is authenticated for http://webapp.
Failure authenticating with NTLM <any realm>@website:80
2017-05-09 09:27:31,248 [Thread-344] INFO User - Authenticating user: domain\user2017-05-09 09:27:31,248 [Thread-344] DEBUG DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.02017-05-09 09:27:31,248 [Thread-344] DEBUG DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.12017-05-09 09:27:31,248 [Thread-344] DEBUG DefaultHttpParams - Set parameter http.protocol.cookie-policy = compatibility2017-05-09 09:27:31,249 [Thread-344] DEBUG MultiThreadedHttpConnectionManager - HttpConnectionManager.getConnection: config = HostConfiguration[host=http://website], timeout = 02017-05-09 09:27:31,249 [Thread-344] DEBUG MultiThreadedHttpConnectionManager - Getting free connection, hostConfig=HostConfiguration[host=http://website]2017-05-09 09:27:31,249 [Thread-344] DEBUG HttpMethodDirector - User defined 'Authorization' headers present in the request.2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "GET /*/5641872227961592590 HTTP/1.1[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG HttpMethodBase - Adding Host request header2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "Accept: */*[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "Referer: http://website/[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "Accept-Language: en-US[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "User-Agent: Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.1; WOW64; Trident/7.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; .NET4.0E)[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "Proxy-Connection: Keep-Alive[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "Cookie: __AntiXsrfToken=7c6d99760df54b609acbd788b9cf127b[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "Authorization: Negotiate TlRMTVNTUAABAAAAl4II4gAAAAAAAAAAAAAAAAAAAAAGAbEdAAAADw==[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "Host: website[\r][\n]"2017-05-09 09:27:31,250 [Thread-344] DEBUG header - >> "[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG header - << "HTTP/1.1 401 Unauthorized[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG header - << "Content-Type: text/html; charset=us-ascii[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG header - << "Server: Microsoft-HTTPAPI/2.0[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG header - << "WWW-Authenticate: Negotiate TlRMTVNTUAACAAAACAAIADgAAAAVgoniGMoCQLWWIkYAAAAAAAAAAKgAqABAAAAABgOAJQAAAA9FAFYATgBUAAIACABFAFYATgBUAAEAFABCAEUARAAtADkAOQA1AC0AMgAwAAQAHABlAGEAdABvAG4AdgBhAG4AYwBlAC4AYwBvAG0AAwAyAEIARQBEAC0AOQA5ADUALQAyADAALgBlAGEAdABvAG4AdgBhAG4AYwBlAC4AYwBvAG0ABQAaAHcAaQBuAHIAbwBvAHQALgBsAG8AYwBhAGwABwAIAJQLcwLIyNIBAAAAAA==[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG header - << "Date: Tue, 09 May 2017 13:27:30 GMT[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG header - << "Content-Length: 341[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG header - << "[\r][\n]"2017-05-09 09:27:31,252 [Thread-344] DEBUG HttpMethodDirector - Authorization required2017-05-09 09:27:31,252 [Thread-344] DEBUG AuthChallengeProcessor - Supported authentication schemes in the order of preference: [ntlm, digest, basic, ntlm]2017-05-09 09:27:31,252 [Thread-344] DEBUG AuthChallengeProcessor - Challenge for ntlm authentication scheme not available2017-05-09 09:27:31,252 [Thread-344] DEBUG AuthChallengeProcessor - Challenge for digest authentication scheme not available2017-05-09 09:27:31,252 [Thread-344] DEBUG AuthChallengeProcessor - Challenge for basic authentication scheme not available2017-05-09 09:27:31,252 [Thread-344] DEBUG AuthChallengeProcessor - Challenge for ntlm authentication scheme not available2017-05-09 09:27:31,252 [Thread-344] WARN HttpMethodDirector - Unable to respond to any of these challenges: {negotiate=Negotiate TlRMTVNTUAACAAAACAAIADgAAAAVgoniGMoCQLWWIkYAAAAAAAAAAKgAqABAAAAABgOAJQAAAA9FAFYATgBUAAIACABFAFYATgBUAAEAFABCAEUARAAtADkAOQA1AC0AMgAwAAQAHABlAGEAdABvAG4AdgBhAG4AYwBlAC4AYwBvAG0AAwAyAEIARQBEAC0AOQA5ADUALQAyADAALgBlAGEAdABvAG4AdgBhAG4AYwBlAC4AYwBvAG0ABQAaAHcAaQBuAHIAbwBvAHQALgBsAG8AYwBhAGwABwAIAJQLcwLIyNIBAAAAAA==}2017-05-09 09:27:31,253 [Thread-344] DEBUG HttpMethodBase - Buffering response body2017-05-09 09:27:31,253 [Thread-344] DEBUG HttpMethodBase - Resorting to protocol version default close connection policy2017-05-09 09:27:31,253 [Thread-344] DEBUG HttpMethodBase - Should NOT close connection, using HTTP/1.12017-05-09 09:27:31,253 [Thread-344] DEBUG HttpConnection - Releasing connection back to connection manager.2017-05-09 09:27:31,253 [Thread-344] DEBUG MultiThreadedHttpConnectionManager - Freeing connection, hostConfig=HostConfiguration[host=http://website]
2017-05-09 09:52:12,938 [ZAP-ProxyThread-100] DEBUG HttpMethodDirector - User defined 'Authorization' headers present in the request.2017-05-09 09:52:12,938 [ZAP-ProxyThread-100] DEBUG HttpMethodDirector - Authenticating with NTLM <any realm>@website:802017-05-09 09:52:12,938 [ZAP-ProxyThread-100] DEBUG HttpMethodDirector - Ignoring authentication, user defined 'Authorization' headers present in the request.2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "GET /bundles/modernizr?v=Vd40cG5fYxxjdknf_y9ilK-zi7pnjL35tk9IAsOQgQc1 HTTP/1.1[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG HttpMethodBase - Adding Host request header2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Accept: */*[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Referer: http://website/[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Accept-Language: en-US[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "User-Agent: Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.1; WOW64; Trident/7.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; .NET4.0E)[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Proxy-Connection: Keep-Alive[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "If-Modified-Since: Tue, 09 May 2017 13:49:33 GMT[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Cookie: __AntiXsrfToken=7c6d99760df54b609acbd788b9cf127b[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Pragma: no-cache[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Authorization: Negotiate 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[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "Host: website[\r][\n]"2017-05-09 09:52:12,939 [ZAP-ProxyThread-100] DEBUG header - >> "[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "HTTP/1.1 401 Unauthorized[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "Content-Type: text/html[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "Server: Microsoft-IIS/8.5[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "WWW-Authenticate: Negotiate[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "WWW-Authenticate: NTLM[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "X-Powered-By: ASP.NET[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "Date: Tue, 09 May 2017 13:52:12 GMT[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "Content-Length: 1293[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG header - << "[\r][\n]"2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG HttpMethodDirector - Authorization required2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG AuthChallengeProcessor - Using authentication scheme: ntlm2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG AuthChallengeProcessor - Authorization challenge processed2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG HttpMethodDirector - Authentication scope: NTLM <any realm>@website:802017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG HttpMethodDirector - Credentials required2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] DEBUG HttpMethodDirector - Credentials provider not available2017-05-09 09:52:12,941 [ZAP-ProxyThread-100] INFO HttpMethodDirector - Failure authenticating with NTLM <any realm>@website:80