For me it happens without ever touching the resolution settings. I have
a notebook with an external display attached (permanently!). The
resolution is already set correctly at the GDM login. But after login,
the applets are mixed up (panels are at their correct locations most of
the time). This even occurs if I "lock" them to their positions.

As already found out, if I use "expanded" panels, there are minor mixups
such as two applets which switched locations. But I recently changed to
"non-expanded" panels and I got a nice puzzle game after the last
reboot... all applets where mixed wildly.

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GNOME Panel icons (on right side) move apparently randomly on session start in 
some situations
https://bugs.launchpad.net/bugs/44082
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