Do you have the OmniFocus mail rule installed? I'm betting that OmniFocus is being launched when the applescript is fired up to handle one of the new messages.
We had another thread about the '2 copies launching' phenomenon a while back; it didn't reach a clear resolution, but some of the info there may help determine what's happening in your case, as well.
Check
here for more info. Try the steps Ken mentions in his post from 3/11 and let us know the results.