FC6 rocks, thats the first thing that i'd have to say about FC6. All most everything worked fine for me, except my IDE did not work. I use NetBeans 5.5 for some of my development work. Since FC6 came with the compiz and it had some good eye candy options, I had it enabled.
My other Java based applications (desktop apps) did not work as well. I did not get any errors. Just that The display was f*cked up. So next I installed KDE (I don't know why), and gave it a try. Seemed it was working fine with KDE. hmmm! So after a little look up, I realized that it was a problem with Java Swing when run under compiz wm. Or its a problem with compiz? I don't think thats the case. But it does not work, unless you have the desktop effects disabled. So no more eye candy. I am not sure if this is the same with XGL, my my guess is it will be.
Likely its related to the some problem with the Swing/AWT? Not so sure. But I am sure there will be workarounds to fix this problem.