I've had this problem with debugging for many years although it seems to be more repeatable now. I'm using Visual Studio to debug x86 ClearWin+ code and with anything other than the simplest of programs if there is a crash within the code, or if I set a breakpoint and then hit the stop button in the IDE to end the session, while the debug session stops the application is left activate, although in a zombie state. This means I have to restart Visual Studio to force the application to terminate to recompile.
I've always assumed it's a fact of life with Visual Studio (it doesn't appear to be a problem when using sdbg), particularly on a 64-bit OS but if anyone has a workaround I'd be interested to know about it (or maybe it's only me!).
Cheers, Alan