Welcome to the forum! I realize this reply is a bit tardy, but I just noticed this post while searching for a different PowerFlex issue.
There is a bit of a gap in your details, so let's fill in some blanks:
What are you using to control the VFD: drive logix, PLC, hard wired controls, etc.?
Can the VFD be set up for Flux Vector control rather than V/Hz?
When you say stop, do you mean a drive stop command was issued? If so, the drive isn't controlling the motor in this state, it's just along for the ride.
It sounds to me like you are stopping this motor while it's still loaded and there's no mechanical brake. If that's the case, I'd expect it to drift eventually.
I haven't had a setup like this more than once or twice but I recall having a mechanical brake on the motor shaft when the motor was stopped. Otherwise, when position was achieved, the drive was kept running in speed mode and the speed setpoint was determined by the position error in order to hold the motor in place. Flux Vector control would be the way to fly here.