Maybe I'm the only one with this problem or maybe everyone else figured it out a while back, but ShutdownObs.js does not seem to allow APCC to properly close its virtual ports. Each time APCC restarts, it has to create new, higher numbered virtual ports and the older ports remain "active" and unuseable. After some advice from Ray G. at A-P, I modifed APCC to auto shutdown after disconnection (this is a choice in the "advanced" tab of APCC). I then modified ShutdownObs.js so that it does not shut down APCC. As soon as ACP disconnects from APCC, APCC starts its own autoshutdown routine and closes automatically, properly closing the virtual ports. So far, this seems to have fixed the problem.