The wheel sets can... not be seated fully, causing an issue like what I believe to be that you're describing. I have not seen a warped truck casting yet after working on a lot of MTH engines. When you remove the bottom cover on the 3/2 trucks, you can see the offending one usually. I also place a straight edge against the wheels to make sure they're all in line.
Make sure the "bushings" are in the correct clock position to make contact with the small tab cast in the truck, underneath them.
