I suppose either one of those scenarios (differences in computers or bad computer) are possible. However, there isn't nearly enough information given to know. A couple of suggestions:
1) When the CEL comes on, that means the computer wants to tell you what problem it is seeing. I think the best first thing to do is pull codes and see what problem(s) the computer is seeing. If you want to try pulling codes yourself, review my "notes on pulling EEC-IV trouble codes"
2) Regarding the differences between computers, do you know if there is a difference between the computers? I don't know how many different "computers" Ford put into a '91. Obviously if one was an auto tranny, the other manual, they would have different computers. I don't know how many different calibrations Ford supplied. Best way to know if there is a difference between computers is to look at the part number and calibration code on that should be attached to the computer. If the two computer have the same codes, then there should be no difference between the two. If they have different codes, then there may be some minor differences, and we can explore that possiblity.