Finally resolution to the issue, I spent an hour and twenty minutes on the phone waiting to talk to a representative from boston. I hung up, called back and still a wait. So two options, continue on hold for hours on end or go to the office in Worcester ( the closest office to me) 45 minutes away. I spent an hour waiting in line, which is pretty good when you figure there are two people running the counter. I explained my situation to the actual person, 15 minutes later left with a new registration and decal for the boat.
Two reasons I didn't want to wait, one anyone on the phone can make promises, I didn't want to wait another 2 weeks for registration I already paid for, plus I cannot use the boat as the temporary registration is only valid for 15 days. I didn't have my decal either. Yes I could have waited and ran the boat anyway but not doing anything would have been worse as its been 24 days since I paid them, any longer they may not have reissued the decal without payment.