Okay, here comes my oldest train story. I went up to my local Two Guys from Harrison after Christmas in 1966 (I was 14). On the shelf behind the counter was a 2322 Virginian that had been returned because it wouldn't run. It would just sit on the track and not move when power was applied.
I knew my dad was pretty adept at fixing trains so I asked what they would sell it for. I think I bought it for around $40 (Catalog price was $65) but swore to my dad that I only paid $25 (I don't think he ever believed me).
The point of all this is, I brought it home and my dad opened it up. When he lifted each end up, the trucks would run. He quickly diagnosed that the factory had wired the two motors in reverse of each other. A quick switch of the wires on one of the motors, and that engine ran great, and still does to this day. You may want to check to see if this might be the same issue causing your problem.
LionelFlyer