Let's not pay too much attention to SelectedFramesFiddler.cap for now.(I included it in case it might shed light on things. I am not actually using the standalone fiddler application in what I'm building.)
So between SelectedFramesFiddlerCore.cap and SelectedFramesNoFiddler.cap, you verified that Chunked Transfer encoding is in use. I understand what you are saying about the TCP/IP packets, but bear with me for a moment:
For SelectedFramesNoFiddler.cap, if I drill all the way down in the Network Conversions Tree view and filter only by HTTP protocol, I see this:
4 11:11:43 AM 6/5/2013 11.1753195 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP: {HTTP:3, TCP:2, IPv4:1}
6 11:11:44 AM 6/5/2013 11.2563155 ReplayTool.exe 131.253.12.52 10.123.3.6 HTTP HTTP:Response, HTTP/1.1, Status: Continue., URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
7 11:11:44 AM 6/5/2013 11.2973307 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
9 11:11:44 AM 6/5/2013 11.6621983 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
11 11:11:44 AM 6/5/2013 12.0271864 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
13 11:11:45 AM 6/5/2013 12.3922338 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
15 11:11:45 AM 6/5/2013 12.7571569 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
17 11:11:45 AM 6/5/2013 13.1221992 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
19 11:11:46 AM 6/5/2013 13.4872242 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
21 11:11:46 AM 6/5/2013 13.8522364 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
23 11:11:46 AM 6/5/2013 14.2172258 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
25 11:11:47 AM 6/5/2013 14.5822563 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
27 11:11:47 AM 6/5/2013 14.9472912 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
29 11:11:48 AM 6/5/2013 15.3123098 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
31 11:11:48 AM 6/5/2013 15.6772954 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
33 11:11:48 AM 6/5/2013 16.0423335 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
35 11:11:48 AM 6/5/2013 16.0434200 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
37 11:11:48 AM 6/5/2013 16.0468752 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
39 11:11:49 AM 6/5/2013 16.8206507 ReplayTool.exe 131.253.12.52 10.123.3.6 HTTP HTTP:Response, HTTP/1.1, Status: Ok, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
41 11:11:50 AM 6/5/2013 17.5137284 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP: {HTTP:3, TCP:2, IPv4:1}
43 11:11:50 AM 6/5/2013 17.5712704 ReplayTool.exe 131.253.12.52 10.123.3.6 HTTP HTTP:Response, HTTP/1.1, Status: Continue., URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
44 11:11:50 AM 6/5/2013 17.5713666 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
46 11:11:50 AM 6/5/2013 17.9364266 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
48 11:11:51 AM 6/5/2013 18.3013842 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
50 11:11:51 AM 6/5/2013 18.6664455 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
52 11:11:51 AM 6/5/2013 19.0314275 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
54 11:11:52 AM 6/5/2013 19.3965122 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
56 11:11:52 AM 6/5/2013 19.7614824 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
58 11:11:52 AM 6/5/2013 20.1271160 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
60 11:11:53 AM 6/5/2013 20.4920897 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
62 11:11:53 AM 6/5/2013 20.8570939 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
64 11:11:53 AM 6/5/2013 21.2221369 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
66 11:11:54 AM 6/5/2013 21.5871414 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
68 11:11:54 AM 6/5/2013 21.9521420 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
70 11:11:54 AM 6/5/2013 21.9529404 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
72 11:11:55 AM 6/5/2013 22.2835550 ReplayTool.exe 131.253.12.52 10.123.3.6 HTTP HTTP:Response, HTTP/1.1, Status: Ok, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
Now, for SelectedFramesFiddlerCore.cap, if I drill all the way down in the Network Conversions Tree view and filter only by HTTP protocol, I see this:
4 11:16:53 AM 6/5/2013 55.4242505 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP: {HTTP:3, TCP:2, IPv4:1}
5 11:16:53 AM 6/5/2013 55.4242951 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
26 11:16:57 AM 6/5/2013 59.3540088 ReplayTool.exe 131.253.12.52 10.123.3.6 HTTP HTTP:Response, HTTP/1.1, Status: Ok, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
28 11:17:03 AM 6/5/2013 65.5836170 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP: {HTTP:3, TCP:2, IPv4:1}
29 11:17:03 AM 6/5/2013 65.5836513 ReplayTool.exe 10.123.3.6 131.253.12.52 HTTP HTTP:HTTP Payload, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
48 11:17:05 AM 6/5/2013 67.5919264 ReplayTool.exe 131.253.12.52 10.123.3.6 HTTP HTTP:Response, HTTP/1.1, Status: Ok, URL: /speech/query {HTTP:3, TCP:2, IPv4:1}
When I said "The request body is chunked over many frames.", this was the difference I tried to highlight. For SelectedFramesFiddlerCore.cap, if you go up one level in the Network Conversions Tree View to include the TCP traffic, it seems like all the request body is transferred in TCP Protocol. However for SelectedFramesNoFiddler.cap, it seems like the request body is transferred to the Server in these HTTP Payload calls on HTTP Protocol, and the server is giving some sort of acknowledgement in TCP Protocol after each HTTP Payload.
I was expecting to see the Netmon capture, at the HTTP Protocol filter, to match for both the FiddlerCore and none Fiddler case. Is this an incorrect assumption?