Sorry for the long delay, I was out of town for a few days.
I think I may have figured out what the issue and rather then blindly trying to post a fix that may or may not address the bug you are experiencing, can you provide some more information such as the steps you took so that I can replicate the bug. Also from what version to what version of Factorio were you trying to upgrade, from what to what version of Manufacturing you were trying to upgrade, as well as a copy of the savegame, so that I can test the fix.
Regardless of what, I plan to roll out what I think may be the cause of the bug you are experiencing. I just what to make sure I am addressing your bug.