When you swapped the drive, did you also swap the resistors? When the load is negative, the load driving the machine, the braking resistors bleed off the excessive current and voltage. This slows the machine and controls the current.When the load is positive, the machine pulling the load, the braking resistors aren't being used. This keeps the DC buss at a constant voltage. Sounds like one of the braking resistors is open.
Exactly. Also if you have swapped to drives it may be just be the drive that is faulty. I would however check all the setting with the other esc and make sure they are the same, and check the dynamic braking resistors are all ok. Your not even using the slow down part of the s curve which is where the braking resistors are really used, so that's where to chopping of the output occurs as Johnny has posted.