If the other thermisters have not been changed (2 in freezer, 1 in FF) they need to be, as the thermister design has beed updated. Also, it may be normal to find a cut wire on the J2 plug, since the instructions that come with the new motherboard says to cut this wire on certain units (it goes by serial number). I believe it eliminates one of the lesser used thermisters, such as the ambient temp one on some models. If the thermisters do not have a blunt end on them, they need to be replaced.
The one in the FF section is part of a damper kit, and can also cause the board to go into pre-chill as you described, however, the usuall complaint is frozen veggies and eggs in this case.
What are the temps running in this unit?