The only thing I can think of is if you’d previously set some window properties for applications i.e. size and position.
The reason I mention this is, some time back, my panel popups (including the calendar, menu, notifications etc.) were appearing in odd positions (i.e. not “attached” to the panel like you’d expect) due to an upgrade conflicting with previous settings I’d made. Clearing those configurations fixed these things for me.
I perhaps should have mentioned it on the Forum at that time, in case anyone else had a similar issue.