I really love Windowblinds, but it really is a PITA at times. One thing that might be useful would be some sort of list of programs that are incompatible, or that need workarounds applying in order to get them working. I've noticed that some skins are less compatible than others too, for instance, Encounter seems to foul things up a lot more often than other, more simple skins.
Could we have a thread where people can report their incompatible app, the skin they were using and their version of Windowblinds/Windows? I think this would go a long way to improving the quality of the program.