I've successfully tested 3.99.0.2 with Symantec Endpoint Protection (11.0.6 MP3) on Windows 7 x64, I haven't been able to use any version later than 3.01-13 with SEP on W7 x64 until 3.99.0.2.
Also no problems with Microsoft Security Essentials, but MSE has worked with all versions of x2goclient that I've tested.
Thanks for tracking this down and fixing it!
Cheers, Daniel