All projects within your suite run this same app I'm assuming?
I wonder, with regards to your VM, if the problem is that the process for the application is remaining memory resident after you close it. So, when you go to execute the tests and run the application, it says, "Oh, there's already an instance running, I'll just wait for it to become responsive", hence the wait message.
I would add some logging into your tests, just to debug. Right before you call the command to run your tested app, do an "If object" Exists check to see if the process is memory resident. If it is, log a message and then call the process's "Terminate" method and see if this resolves your problem.