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My name is ***** ***** I am a professional here at Just Answer. I noticed that your question had not received a response and thought I would see if you still need help with this.I apologize for the delay and I hope I can still assist you with this here.
This can be due to a fault with a failing micro switch/sensor that detects the position of the roof.It can cause the roof to continue to run like you see.I would have the fault codes checked with a compatible scan tool/computer plugged into your vehicle to see what codes are set.Once this is done any codes set then need diagnosed to help locate the fault.I would also use a scan tool to see if you can read the sensor signals from the roof components to see if you can locate a faulty position sensor.In allot of cases it is built into the roof motor and sometimes a relearn of the roof system with a scan tool will resolve this and in other cases the motor may need replaced.It is usually a hall sensor in the motor itself.
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