Did you try cleaning the rotary switch once? It might be just the switch not making good contacts.. If not, it could be a problem with one of the sunroof guides on left or right side. Does the sunroof binds when it gets stuck at that position? There is a good chance that the broken plastic pieces from the guide are lying on the sliding track which can restrict the movement of the glass on the track. This was the problem in my car last year where the track was filled with bombarded cheap plastic pieces causing sunroof to not close once its opened. Watch video here from my car(
https://www.youtube.com/watch?v=MTc0hebfVZs). So in your case,you have to remove the glass and then inspect both guides for any damage. You will also need to check the guide track(use a small paint brush or something) to clean up any plastic debris lying in it.
The sunroof guide will look like this below, you can see the broken plastic on the guides. Note the position of the small guide marked 'A' at the middle. This is the position of the guide when the sunroof is level with the roof.
Now in this second pic, the center guide 'A' has moved to the front raising the guide at the other end. This will be the position of the guide when we tilt the the sunroof upwards.
And in this third pic, the center guide 'A' is at the extreme left end of the guide and you can see that the height of the guide is now lowered more compared to the first and second setting above. The guide is lowered more here to lower the glass below the roof level so that it can slide to the back side when we actually open the sunroof. This position occurs only when we open the sunroof. And this where exactly your problem is.... For some reason the center guide is not making its way back to the middle position(first pic above) when you close the sunroof causing the glass to sit below the roof level. As I sated earlier, it could be just the plastic on the guides are damaged preventing free movement of the center guide piece A. Or the broken plastic pieces are coming in the way of the guide.. These can be fixed if you remove the glass from the top and then inspect the guides and track. But if your guides and tracks are okay, then it could be the actual cables causing the problem which is a PITA to fix..
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