Your problem may be the result of a "vertical curve" that's too sharp. Though aware of horizontal curves, few people are aware of the vertical curves that we encounter every day as we roll up and down hills on the highway - they're just "hills". However, they can be a big problem on railroads because the wheelbases are much longer than those of private automobiles and the couplings have to flex, too.
Ensure that your vertical curves (transitions) are nice 'n' gentle, taking place over multiple car/engine lengths.
