The problem is likely that the turnout is twisted -- i.e., the three legs of the turnout are not in the same plane. You should not have a grade going through the turnout as rigid-frame locomotives will take issue with it and some of the wheels will lift out of the track. We had a problem like that with a Ross #8 curved turnout (O-96/O-120) and I had the fun task of realigning the whole area.
also the tracks leading into and out of the turnout must be on the same plane as the turnout. if this is your problem then if you look closely and run slowly and you will see a wheel lift out of the track. I have seen this often when a grade change takes place near a turnout. the centipede tender on my FEF is a good model to test if you are on a flat plane as you enter and leave.
