MxxCon, we found the problem...
We use a generic service account to run these scheduled tasks. Someone had used that login at the physical server which is not our normal procedure because we normally remote it. So what happened is another user logged in remotely with the same service account and the flash instances showed the remote session that flash was running as a process while the flash application windows were popping up at the console session. Live and learn, I hope this helps someone else that has this happen.
Thanks,
Bryan