I posted this as a bug at the sourceforge project, but posting a summary here because I'm not sure how often the (until-now-empty) bug list there is checked:

When I close the win32 version of Bitcollider (v0.3.1), on Win98, it apparently doesn't release focus properly, because explorer.exe functions (alt-tab, windowskey, etc.) don't work, and attempting to use them sometimes causes a crash, usually in kernel32.dll. However, if I click anywhere on the screen first (thus switching focus to whatever I clicked on), everything works fine, and there are no crashes.

I just accepted that bug. Thanks for reporting it.

I added a comment that said:

Interesting -- how did you invoke the bitcollider?

Does the behaviour change when you invoke the bitcollider from the desktop vs. from the right click menu?