The higher the voltage you run the motor, the higher the rate of rise of the current through the windings.
The integrated PWM current regulator might have a minimum on time. Also, the current limiter will have an associated delay to it, so you should not rely on current limiting to tame the PWM regulator. In other words, I suspect your RMS current through the motor, coupled with the high supply voltage causes excessive power dissipation.
Try using a motor with higher winding inductance - usually more turns and higher voltage. That will also increase your torque and reduce your current drain.
Alex