Could be a lot of things. I find that help working out the problem I get a trend with the motor torque, Speed and acceleration and Position Error, Position feedback.
Could be Zero speed hunting, Gear Binding, Stopping at a position where you are pushing against an end stop, ramp rates, ie lots of things.
Kinetics
To get the Torque and Position Error you must
1) Set Axis Properties -> Drive Motor -> Real time Axis information Attribute 1 or 2 to Torque Command OR Torque Feedback and the Other to Position Error
2) Also in the Motion Group Properties
Set Attribute Auto Tag Update to "Enabled"
Once you have the trend post a jpg for more help
Note: you can also monitor the "Motor Capacity" which i think is the thermal model for the motor as a %
