Mathematica's front-end is not guaranteed to work through any particular remote-access program.
I added you two to the existing suggestion for supporting X2Go.
I'm experiencing this issue now only Mathematica -mesa is not working for me. Does Mathematica -mesa work for anyone else in X2Go or has it been broken in newer releases?
Have you tried -clean or -defaultvisual ?
Is this also with Mathematica 9?
Yes, Yes and Yes :(