Aha! I may have solved it. I was repeatedly getting this error: "Do you want to scan and fix ipod?" It would also open a window (several times) asking me what I wanted to do - open the folder or speed up my system. Fix for the first issue is here:
http://www.futureofrealestatetechnology.com/general-real-estate-technology/resol ve-vista-scan-and-fix-error-when-plugging-in-ipod-or-other-devices/
Fix for the second issue is to turn off autoplay. (setting everything to "take no action" wasn't enough)
Sorry that I wasn't more complete with my description of the problem. I was super tired when I wrote it. I forgot to even mention that the system is running Vista SP1.
Well I am hoping that this will fix everything. It really did seem like a loose connection because those windows would pop up several times
especially if I tapped the ipod, so I figured it was basically reconnecting over and over again. Also it would interrupt syncing, but that hasn't happened since I restored it to factory defaults and tapping it seems to no longer cause anything bizarre to happen (not even with iTunes up). The tapping issue may have just been a coincidence - I may have
thought tapping it was causing something to happen but in fact those windows may have just been coming up on their own.