I've noticed than in my filesystem tree there were some empty folders under \PCL that seemed to be some filesystem reorganization leftovers. Just to make sure I wiped the directory (which I usually don't do before upgrades) and reinstalled the application, just to see the directories go away.
So my suggestion is to add a little paragraph in the web site about upgrades and the convenience of deleting the directory. I haven't had any problems caused by this so far but who knows if some bug is there awaiting to bite us in the future...
BTW, the installation system is just great. It couldn't be cleaner. I hope it will stay so!