I'm using x2go Windows client 3.99.2.0-rc2 and also the Ubuntu client, connecting to Ubuntu 64-bit x2go version 2:3.5.0.12-0~234~oneiric1, using both gnome-session-fallback and unity-2d sessions.
With certain client programs, especially Eclipse, I have noticed a very long delay when a redisplay of the underlying program window is necessary. For instance, when a dialog box that overlaps the main Eclipse window is closed, or a terminal window is put underneath Eclipse, there can sometimes be a 5-30 second delay before Eclipse redraws itself. During that time the whole x2go session is frozen. I looked in all the relevant logs and see nothing.
I am not sure this is an x2go problem at all, but I don't remember similar problems with Eclipse and freenx. I've looked for similar Eclipse bugs, but all the ones I found that sounds similar are quite old and supposedly have been fixed.
If you have seen this problem with Eclipse or other client programs, I'd be interested to hear about it and if you have a fix.
Thanks, Dan