I guess this is the new transparency code. You can try to recompile with
it disabled (change the --enable-argb to --disable-argb in debian/rules)
and see if you have the same problem. I don't use Gnome myself so I
can't test (works fine for me).
** Changed in: conky (Ubuntu)
Status: New => Incomplete
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Conky hides itself behind nautilus desktop
https://bugs.launchpad.net/bugs/537499
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