vic, I actually just ran into that same error. It's actually a very nice feature of the program that GT put in. If the incoming script is running, it has the mailbox open, so the script always checks to see if it's already running before trying to open the mailbox.
Do you always see the same pid: 3939 or does it keep changing? If it keeps changing you probably have cron set up to check too often, in that it doesn't finish sorting out the mail before it's ready to start again. add a few minutes to how frequently it is being checked now. If it's the same pid, then something else is wrong, it shouldn't be running that long.. I'm not sure what to do there, maybe GT can help.
PS - there another typo, Qutitting...