I don't think this is just a problem with Pidgin.  I use Gajim and
Evolution in the widget layer.  If I get a notification, the widget
layer disappears (see https://bugs.launchpad.net/ubuntu/+source/notify-
osd/+bug/346467), if I click on the title bar of any of the windows the
widget layer disappears
(https://bugs.launchpad.net/ubuntu/+source/compiz/+bug/356374), tooltips
in either application cause the widget layer to disappear.

Long story short, this is probably not a Pidgin-specific bug.

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Pidgin in Compiz widget layer deactivates on tooltip creation
https://bugs.launchpad.net/bugs/357460
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