This happens to me, actually pretty much every time I log in. For me,
the situation is that my laptop's screen runs at 1280x800 and my
external monitor runs at 1920x1200, and I switch between the two all the
time mid-session. I never use twinview; I just disable one monitor and
enable the other.

This is with The Default Panel Configuration in Jaunty. I usually just
delete those launcher applets and leave it be. I kept an eye on the
panel configuration with gconf-editor.

Initially, applets are placed correctly as copied from default_setup...
/apps/panel/default_setup/applets/notification_area:
locked:1
panel_right_stick:1
position:5

Note that each applet is placed from right to left, with "position"
incrementing from 0 where 0 is rightmost.

I checked later (sorry, STILL hunting for the pattern) and found this...
/apps/panel/applets/notification_area_screen_0:
locked:1
panel_right_stick:0 (!!!!!!!!!!!!!!!!!!)
position:1279

The bottom panel also falls apart in the same way. They both do so at
the same time.

I tried starting the positions on the right side from 1 instead of 0, but it 
made no difference. I also tried positioning only the clock and the Hamster 
applet on the right, which did no good.
( Although it looked cleaner with the notifications beside the menu :) )

Notice that the posititons end up relative to the positions on my
laptop's screen, but also a little bit off.

-- 
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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