Dave:
I'm sorry, I don't have an answer for that problem. It did it to me also when I was trying to control the scanner from within Amazing Charts. I never figured out how to stop it and ultimately started scanning and organizing my files *outside* of Amazing Charts with ScanSnap Organizer (came with my Fujitsu scanner), which setup I have been very happy with. (I am scanning old records as searchable PDFs, which is pretty cool).