We had a couple of updates to address this issue. Can you please report,
if this is still an issue for you? I've a nvidia/twin-view setup here
too and with notify-osd 0.9.11 it works flawlessly for me.
** Changed in: notify-osd (Ubuntu)
Status: Confirmed => Fix Released
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Bubbles appear on top of panel when using twinview
https://bugs.launchpad.net/bugs/353933
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