I recently had to re-install LiteStep, and after I got it updated back to the final build, it started behaving strangely with respect to things on the desktop. I have Rainlendar, Rainmeter, Miranda, and Foobar in the four corners of my desktop. When LiteStep is running, all but Foobar disappear. I'm not sure if they're going off-screen or what, but even restarting the programs in question don't bring them back. I quit LiteStep, and there they are again. What's going on?

Oh, it seems it was also messing up DirectX. I was getting errors when testing DirectDraw and Direct3D with LiteStep running, but when I reverted to Explorer as the shell, they went away.

does clicking on the desktop "fix" the disapearing problem? Does unloading the desktop, or unloading the VWM module fix the disapearing problem?

Ensure you don't have a transparent pixel at 0,0 for the directx issues.