I've got a similar problem that I think is related.
randomly (about 50%) of the time when I change screen resolutions the panel will move from the bottom
of the screen to the top then disappear.
I can't get them back for anything without deleting them rebooting and then recreating them from defaults.
what appears to be happening is that the panel paints at the top then shifts up a panel width and is stuck up there just beyond reach. I have watched the RSS feed applet move up and down in the same way as you move the panel to top or bottom.
When the panel disappears I can watch the little RSS feed shift up a panel width allowing space for the panel to paint below it. But it doesn't. It paints at the top. Then it shifts just like any other little app and disappears.
I think it's tied to the refresh and change of screen resolution. I startout with the logon screen at 600/800 (which I hate by the way) then as soon as I login it changes to 1600x1050 and all is well till the panel shifts.
I think If I could get the logon screen to start at 1600x1050 it wouldn't happen as often. but I can replicate this almost at will if I change screen resolutions. Also when doing that the wall paper will not repaint correctly. (irritation) but probably symptomatic of the same problem.
once the panel shifts up other apps will not come up correctly either (second problem)
So if I start say... firefox it pops up normally but if I click off it then it shifts up above the panel where I can't reach it. I can launch 10 apps and they will all shift up above the panel if I click off of them. They shift as soon as they loose focus.