A couple of quick thoughts:
1. Forgive me if this is too obvious, but confirm that you aren't powering the motor directly from the Mini. I assume this isn't the case, since you had it set up and working previously, but it's one way that a motor would spin when the e-stop was disabled

1. The motor should not run at all if the Mini's ENABLE circuit is connected to your motor amplifier (aka drive). What make & model drive is the Mini controlling? What terminals are connected to the Mini's control pins 2 & 3?
2. Put a meter on the speed control lines coming out of the Mini (pins 1 & 4). The voltage range on these pins is +/-10vdc. With the motor disconnected, power up the Mini and check the voltage on the speed signal lines. The voltage should be around 0V. If it's not, there's a problem with the Mini.
3. Put a continuity tester on pins 2 & 3, the enable pins. There shouldn't be any continuity until you press either the FWD or REV jog buttons. If you get continuity when the Mini is supposed to be idle, there's a problem with the Mini.
4. Are you using the same motor amplifier (aka drive)? If not, it could be that the drive needs to be calibrated. Many drives have a MIN SPEED setting that is sometimes not set to 0.
Hope that helps with some troubleshooting ideas, let me know what you find.
Gareth Conner