I've also experienced this problem (sometimes I found that Dexpot will put the top of a window at the very bottom left of my right monitor (running dual monitors). Couldn't make the problem happen reproducibly though.

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Running Windows 7 Pro x64 SP1, dual monitors, Dexpot Version 1.5.99, Build 1776

I tried playing around with it for an hour and a half, and I can reproduce the problem >20 times, but I still can't pin it down precisely. It takes ~2 min to get it to happen. -I have tried using readily available windows programs, and it seems to be general (Windows Task Manager, Excel 2010, Google...

Yes, the persistent taskbar is enabled. The icons of the programs running do appear in the taskbar, but when I click on them, nothing happens. I can make it happen with any program, such as Excel 2010, and even System Task Manager. (Task manager requires a system restart, because I can't call a new ...

If I have programs running on other desktops and I hibernate, sometimes those programs become inaccessible. They're still running, but the windows are invisible (they're in the taskbar, but not on any desktop). I can sometimes call them up with "Maximize" command from the Task Manager, but...