Sorry if this is a no no since this thread is so old, and I'm assuming it got fixed since there was no other replies, butI know that this is a common problem that I have some experience with that I figured might help someone.
My sunroof had the same issue and looking over the manuals wasn't helping so I did what any smart diyer would do and took it all apart!
Turns out the plastic gear had slipped. The worst part though, is that our closed open position is completely mechanical and tied to that stupid plastic gear. I found that the "easiest" fix was to grab a new plastic gear box from the junk yard, install it (with the headliner still down), and attempt to open the door all the way.
If it stops short, remove the gear box (and ONLY the box) and CAREFULLY manually pull the sunroof all the way back. Then re- install the gear box and test everything.
If it goes all the way open but won't shut all the way, then remove the glass (4 screws) and the gear box and CAREFULLY manually try to shut the door. There is a lever you need to push on to get it from vent to shut. Some playing around and you should find it. Then re- install and test.
Basically, what you are doing is finding either full open or full shut in the gear box, manually adjusting the roof to what it thinks it is, and then re-assembling.
One way to easily remove the gear box is to remove front four
screws and loosen the rest to tip the roof so you can access the box without having to remove the motor. Just be careful!
The metal sunroof gear almost never strips, it's the gear box. Unfortunately for us, the only way the processor knows what position the roof is in is mechanically linked to that plastic wheel that has metal contacts that complete and close various circuits (open the box and you'll see). I could have figured out what positions mean what, but this way worked for me and is much easier.
And don't forget to lube those tracks while you're up there!
Hope this helps someone.