Because of the way Apple's Spaces work, we have to poll the Space you're activating to get its list of open windows when you open that Space. Depending on which programs you're running, this may lead to a situation where Witch displays a list of windows from the prior Space.

This is most likely to happen if (a) you activate the Witch panel immediately after switching Spaces, and (b) you're running a Java app, or Chrome with Flash pages, or certain other programs that are slow to respond to Witch's "please tell me which windows are open" inquiry. (More details on this issue.)

The fix is simple, if a bit annoying: just wait about two seconds after switching Spaces before activating the Witch panel.