That's really disappointing especially since the update should have fixed this.
I have to file in MA as well and did the workaround with manually overriding/overtyping the entries. I was initially very sceptical but did not want to wait for the update and had about 15 transaction to change manually.
All in, it worked like a charm and I was able to file IRS and MA returns. Both returns were accepted and processed and I even have the refunds already in my account.
That may or may not help your situation, just wanted to share my experience.
Maybe just overriding the numbers for MA is a solution - if you can go back and change the Sched D after filing Federal return already.
Good luck.
