I get the exact same error with munkireport 2.13.0 and it doesn't work with killall cfprefsd.
If I downgrade the server to 2.12.0 the error disappears.
If the client installs the new version the error doesn't show until I run defaults read /Library/Preferences/MunkiReport.plist BaseUrl
If I add $conf['debug'] = TRUE; do my config.php the error disappears.
root# /usr/local/munki/postflight
Munkireport: # Executing scripts in postflight.d
Munkireport: Running inventory_add_plugins.py
Munkireport: Adding 11 plugins
Munkireport: Running managedinstalls.py
Munkireport: Running munkireport.py
Munkireport: Requesting ard
Munkireport: Requesting appusage
Munkireport: Requesting munkiinfo
Munkireport: Requesting homebrew
Munkireport: Requesting profile
Munkireport: Requesting deploystudio
Munkireport: Requesting location
Munkireport: Requesting findmymac
Munkireport: Requesting installhistory
Munkireport: Requesting network
Munkireport: Requesting fan_temps
Munkireport: Requesting bluetooth
Munkireport: Requesting fonts
Munkireport: Requesting displays_info
Munkireport: Requesting localadmin
Munkireport: Requesting directory_service
Munkireport: Requesting munkireport
Munkireport: Requesting gpu
Munkireport: Requesting disk_report
Munkireport: Requesting power
Munkireport: Requesting usb
Munkireport: Requesting inventory
Munkireport: Requesting softwareupdate
Munkireport: Requesting managedinstalls
Munkireport: Requesting sccm_status
Munkireport: Requesting gsx
Munkireport: Requesting security
Munkireport: Requesting filevault_status
Munkireport: Requesting wifi
Munkireport: Requesting network_shares
Munkireport: Requesting homebrew_info
Munkireport: Requesting warranty
Munkireport: Requesting timemachine
Munkireport: Requesting crashplan
Munkireport: Requesting munkireportinfo
Munkireport: Requesting printer
Munkireport: connection_willSendRequestForAuthenticationChallenge_
Munkireport: Authentication challenge for Host:
server.domain.se Realm: None AuthMethod: NSURLAuthenticationMethodServerTrust
Munkireport: Allowing OS to handle authentication request
Munkireport: Need to update reportdata (372B)
Munkireport: Need to update softwareupdate (490B)
Munkireport: Need to update power (4KB)
Munkireport: Need to update homebrew (0B)
Munkireport: Need to update inventory (141KB)
Munkireport: Need to update fonts (531KB)
Munkireport: Need to update gsx (30B)
Munkireport: Need to update usb (4KB)
Munkireport: Sending items (681KB)
Status: 500
Headers: {u'Content-Length': u'34', u'X-Powered-By': u'PHP/5.4.16', u'Server': u'Apache/2.4.6 (CentOS) OpenSSL/1.0.1e-fips PHP/5.4.16 mod_wsgi/3.4 Python/2.7.5', u'Connection': u'close', u'Date': u'Tue, 04 Apr 2017 12:21:51 GMT', u'Content-Type': u'text/html; charset=UTF-8'}