That's a known bug if you've got your taskbar docked to the left or right of the screen. With the taskbar at the bottom of the screen, the popups stay docked.
Same problem I'm having, the wiki says it's fixed in the next version.
Thats nice, but if there will be 5-6 months (maybe years, who know) before the next release....
The problem is, that this block a few things, try dobbleclicking a .reg file to import it into the registry, thats not possible the direct way, since you have to click Allow on a popup that off, and stays off the screen.
These popups spawns as new processes, which means that in a matter of days, there might be 10-20 of them hanging off the top of the screen, each eating about 3-5mb of memory.
Is there a special reason why there hasn't been another beta release in the past 3 months?