That's an interesting find. I will see if I can reproduce the problem when I get back in.
EDIT- Yup, it's definitely doing that. I'm going to have to dig in on this one, as it looks like it's a handle issue (it's losing its handle). I have no ETA on the fix, unfortunately. The only workaround for the time being is to not pass -command line params in for multiple instances when set to, 'minimize to system tray'. Also, if you are running it from a scheduled task, I believe you can have the task kill the running instance if you want it to. Just a suggestion.