Adjust the nuts on the motor drive. They control the point at which the clutch engages/disengages. Adjustment can be a little finicky. Mine started doing the same thing after putting on a new seal that was so much thicker and bulbous that it created a little too much resistance when closing and worked the nuts loose.
Start with those nuts since it's easy, but if that doesn't fix it, there are a couple of micro switches also located on the motor assembly that may be bad. Usually when they go out, the motor will continue to run and drag the steel cable across the plastic gears and yes, that's not good. My guess is that it's the clutch adjustment. Check out Clark's Garage site for a sunroof motor PDF. It's easy to get to in the driver's side rear wheel well.
- Darryl