Hey, this is actually a post of the solution rather than a problem, i searched for this issue for quite a while before i found the cause so i thought i would share.
After confirming that your problem is not just a slipping encoder (mark everything)
The issue turned out to be that the bell housing (where the magnets are) was not properly attached to the shaft anymore, it took quite a bit of twisting with a locking pliers on the motor shaft before i could get it so spin the 2 degrees or so that it would slop back and forth on the shaft, the issue was hard to detect because my mechanical load has the same problem, about two degrees of backlash on the shaft, when i applied load in different directions both the load and the bell housing would slop their 2 degrees over to the other side of the shafts D profile and stop (and stick there pretty well too). This of course causes an offset between the encoder position and the bell housing which is the cause of the heating, and the torque reduction.
In order to loosen or tighten the grub screw on the motor you need to release the locktite that they use on it To do that i cut the top off of a pop can and filled it with water, disassembled the motor and placed just the bell housing and shaft in the water so the water would cover the magnets and allow me to heat the locktite without damaging the magnets.