Need advise on 4T60 issue/replacement
 

Hey everyone. I am a Ford tech, but I have a number of GM's in the family. I been trying to fix my mother in law's 1994 Ciera with a 3.1 and a 4T60 trans. The original trans had a sever delayed engagement but it had all it's gears once it got going. I put an LKQ unit in it 2 weeks ago but while test driving it dropped out of 4th gear into 3rd after about 1 minute and would only give 3 forward gears from then on. I figured it was a bad unit so I called LKQ and got another one. Put it in yesterday and had the same issue. Now I'm thinking its a compatibility issue with the electronics. The first LKQ unit came out of a 95 Grand Prix and had an aluminum side pan whereas my original had a steel side pan. I haven't called them yet to see what this unit came out of but it also has the aluminum side pan. I didn't think anything of it when I installed it, but now I think maybe the ECM sees something it doesn't like and is disabling 4th gear. Any ideas? Are there differences with the 4T60's between car lines and year models? Thanks