I don't use Ubuntu, but if you have both TL2010 and 2011, I'd check the directories that are in fontconfig (or run fc-cache -v and see which directories it's looking in). It may be that fontspec is complaining because it finds duplicate sets of fonts between the two installations. Your PDFs would be OK because the font files are otherwise identical, but you'll likely notice problems if you had different versions of the same font.
As for the other problem with SyncTeX... I can only imagine it's somehow related. Possibly a PATH error? HTH, Andy -------------------------------------------------- Subscriptions, Archive, and List information, etc.: http://tug.org/mailman/listinfo/xetex