This happens to me in 12.10 as well. The background changes to light-
grey "randomly" and then changes back to transparent after a while. I
will try to see if there is a pattern in these changes not to call them
random any more!
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Not mentioning it is a bit hard to start conky up correctly (I have the
famous run after x seconds bash script so it doesn't appear on top of
everything), the background problem appears on opening Nautilus the
first time. I still haven't figured out how to make it disappear by
itself, so what I hav
