If you're sure of that, then the problem is likely to be something like @Braiam suggested in chat, that Unity died while setting something up and did not clean up well after itself, a clear bug. If you still have the files, try running a few
diff
s, they might give more info. By the way, I also tried this with a newly created user, made no changes to his configuration, and was able to log in with no problem after correcting the
/etc
permissions. So, it is almost certainly
dconf
/
gconf
or
compiz
that's being screwed with. —
terdon 17 secs ago