In the absence of taking apart all my AM engines, I'd suggest giving American Models a call and explaining your predicament and asking if there really IS a difference in the gears on the axles. Especially since you have a 1996 date on the chassis. My F40s are about that year too, but I'm pretty happy with the way they perform just like they are, especially since they pull a long string of Superliner cars. Now that I think about it, I have an RS3 that needs an axle gear since it's missing a tooth.
I just thought of something. I once had a U-joint shaft ball that wasn't seated correctly in the socket. Maybe...?