Hi,
I had a problem with text (of certain colours only) suddenly disappearing from windows, and not being visible again until I disconnected and reconnected. This problem has been reported on the FreeNX mailing list, but I didn't see any mention of it here yet. I found that setting the image compression method to png (20M, I think) instead of jpeg, fixed this problem for me (so far). But it might be just a coincidence that I stopped having this problem - on the FreeNX list, some people report that the issue is very intermittent and hard to pin down.
I am using a self-built X2Go Server with the latest NX libraries (also self-built) on the server, and on the client I'm using the standard Ubuntu/Debian packages (on Maverick). Incidentally, the client machine is actually a Virtualbox VM, although I'm not sure this is relevant.
Regards,
Robin Green