Unfortunately this VIN situation is common in many states, particularly with cases in which the motorcycle is the right age (1980 model year or later) to have the 17-digit VIN instead of the 7-digit serial number on the title/registration, but some doofus put the 7 digit number into the system instead of the 17 digit one. I've had to deal with that problem both in MA and in VT. I would hold the MA DMV right up there with the CA DMV when it comes to "sources of extreme aggravation" any day.
I recall when I moved to MA, I had to take the written exams for both auto and motorcycle licensing, but didn't have to take the driving tests as I'd already been licensed to operate all these things in another state. I took both tests and got a perfect score, and waited in line for 45 minutes to get my shiny new license with motorcycle endorsement. I got to the front of the line, and they wouldn't let me get my license until after the full time limit (which was apparently 2 hours) had expired for taking the written tests... apparently if you know the answers and finish early you still had to wait until the maximum test time set in the system elapsed before they'd accept and issue new licenses. This was just one of the many, many silly things in the Massachusetts DMV back in the 90s..