I recently installed Eagle 6.3.0 (using the shell script on Cadsoft's Downloads page) on Xubuntu 12.10 and I'm seeing some problems when trying to draw a schematic or create a symbol, etc. Specifically, the "edit screen" doesn't seem to refresh correctly so I get some whited out areas and copied parts of the image. I've attached a screenshot to show what I mean.
Also note that I installed an older version of Eagle (5.12) through my package manager and the problem existed there as well. This, together with the fact that I have used Eagle on previous installations of Xubuntu (12.04) and have not had this issue leads me to believe that it is something on the Linux side. However, I asked on Xubuntu's IRC channel and another user of Eagle + Xubuntu 12.10 said they do not see the same issue.