have the same problem about the user-agent. My tests are showing an issue when requesting on port 80 and not on other ports. Seems to affect all headers!
see attached screens.
Using the last SoapUI OS : SoapUI 5.2.1
Found a possible reason. On my case, the remote server is responding a 302 redirection to https. On logs, I see the headers sent on the first request to http but not on the https. Seems SoapUI is forgotting the headers after a 302.