Maybe your application hasn't finished loading when you attempt to close it? Can you add another Wait method to confirm the application has finished loading? For instance, we use a WaitWindow to detect that our start window has opened. Other options might be a WaitProperty to verify the application window is enabled, or WaitProperty for a toolbar button to become enabled.
It seems like a timing issue could be the culprit. Just because WaitProcess determines the EXE is running doesn't mean the app is ready for interaction via automation or the user interface.
