David says this is due to wrong compiz default settings:
https://answers.edge.launchpad.net/notify-osd/+faq/386
** Changed in: compiz (Ubuntu)
Sourcepackagename: notify-osd => compiz
Status: Incomplete => New
** Changed in: compiz (Ubuntu)
Importance: Undecided => High
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sometimes notification flickers when fading in
https://bugs.launchpad.net/bugs/331564
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