I sometimes observe this as well (the popup ends up in the top-left
corner of my screen rather than next to the icon). However, I don't
think it could be caused by a race in the MN code, since when I comment
out the code which shows the icon, the popup is still properly
positioned (next to the invisible icon). You might want to submit a bug
report on the libnotify bug tracker.
** Changed in: mail-notification
Status: New => Invalid
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Notification popups not always attached to the icon
https://bugs.launchpad.net/bugs/212778
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