I've just upgraded to jaunty and I am getting similar behaviour when
using audacious on the widget layer.  I can reproduce the effect by
trying to bring up the audacious preferences window.  The preferences
window appears, but the widget layer deactivates and the rest of the app
windows disappear with it.

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Widget layer disappears when interacting with applications within the widget 
layer
https://bugs.launchpad.net/bugs/356374
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