Sounds like you need to "reset" the sunroof. I found this on another Honda forum, so I'm not certain whether any of these will work:
Method 1:
TURN THE IGNITION TO THE ON POSITOIN
1. hold the auto open button and keep holding it until 3 seconds after the roof is open.
2. Hold the auto close button and hold until 3 seconds after the roof is closed.
Method 2: Moonroof glass is positioned in the OPEN position (or partially open)
1. Press the moonroof OPEN switch until the moonroof stops in its fully open position.
2. Release the moonroof OPEN switch.
3. Press the moonroof OPEN switch again for about 13 seconds .
NOTE: Keep pressing the switch even though the moonroof motor continues to function.
1. Calibration is complete. The moonroof will automatically move to the regular preset fully open position and come to stop.
Method 3: Moonroof glass is positioned in the TILT position
1. Press the moonroof OPEN switch until the moonroof glass stops in its fully open position.
2. Release the moonroof OPEN switch.
3. Press the moonroof OPEN switch for about 13 seconds .
NOTE: Keep pressing the switch even through the moonroof glass will repeat an inching behavior (moving 40 mm , then stopping for 0.4 seconds )
1. Calibration is complete. The moonroof will automatically move to the regular preset fully open position and come to stop.
Method 4:
1. Close driver’s door, leave it closed during the whole procedure.
2. Turn ignition to LOCK (0).
3. Press and hold the tilt switch, and turn ignition to ON (II).
4. Release the tilt switch, and turn ignition to LOCK (0).
5. Repeat steps 3 and 4 four times.
6. Check if the AUTO OPEN and AUTO CLOSE function still work. If they still work, the AUTO functions have not been cleared, go back to step 1. If AUTO functions have been cleared, go to step 7.
7. Press and hold the moonroof open switch for at least 3 additional seconds after the moonroof is fully opened.
8. Press and hold the moonroof close switch for at least 3 additional seconds after the moonrood is fully closed (tilted).
9. Confirm that the moonroof control unit is reset by using the moonroof AUTO OPEN and AUTO CLOSE function.
Method 1:
TURN THE IGNITION TO THE ON POSITOIN
1. hold the auto open button and keep holding it until 3 seconds after the roof is open.
2. Hold the auto close button and hold until 3 seconds after the roof is closed.
Method 2: Moonroof glass is positioned in the OPEN position (or partially open)
1. Press the moonroof OPEN switch until the moonroof stops in its fully open position.
2. Release the moonroof OPEN switch.
3. Press the moonroof OPEN switch again for about 13 seconds .
NOTE: Keep pressing the switch even though the moonroof motor continues to function.
1. Calibration is complete. The moonroof will automatically move to the regular preset fully open position and come to stop.
Method 3: Moonroof glass is positioned in the TILT position
1. Press the moonroof OPEN switch until the moonroof glass stops in its fully open position.
2. Release the moonroof OPEN switch.
3. Press the moonroof OPEN switch for about 13 seconds .
NOTE: Keep pressing the switch even through the moonroof glass will repeat an inching behavior (moving 40 mm , then stopping for 0.4 seconds )
1. Calibration is complete. The moonroof will automatically move to the regular preset fully open position and come to stop.
Method 4:
1. Close driver’s door, leave it closed during the whole procedure.
2. Turn ignition to LOCK (0).
3. Press and hold the tilt switch, and turn ignition to ON (II).
4. Release the tilt switch, and turn ignition to LOCK (0).
5. Repeat steps 3 and 4 four times.
6. Check if the AUTO OPEN and AUTO CLOSE function still work. If they still work, the AUTO functions have not been cleared, go back to step 1. If AUTO functions have been cleared, go to step 7.
7. Press and hold the moonroof open switch for at least 3 additional seconds after the moonroof is fully opened.
8. Press and hold the moonroof close switch for at least 3 additional seconds after the moonrood is fully closed (tilted).
9. Confirm that the moonroof control unit is reset by using the moonroof AUTO OPEN and AUTO CLOSE function.
