I've been having very bad scans with my MakerBot digitizer, even Tech support could not find the problem. They sent me a new machine and that had the same "bad scan" problem.
Yesterday my computer could not "find" the digitizer and I remembered having this type problem with a printer. Solution, I changed the USB cable to one with a noise suppressor built in and it fixed the scan problem.
The new digitizer they sent me had a new USB cable with it it so I must assume their cables are a poor quality. I can scan and directly print with very good results now..... So if your having the "scan" problem with your digitizer, try a USB cable with a noise suppressor in line. It worked for me.
Don