98 A6 Quattro 2.8
My moonroof will not shut. I turn the dial to close and it just stays where it is at. If I turn the dial slightly to open, it closes the moonroof all the way. It also seems like it is returning it too far back.
I the turn the dial a little more and it goes to about the 1/3 way shut position.
Problem with the motor?

there is a replaceable module inside the cover where manual close is.
its one of the quirky things in audis.
does it close right when you use the key in the driver door?

I was able to close it manually. I did not close using the key in the door.
Think replacing that module is the answer?

Usually replacing the module will work. It is about $70.00 and is self programming.

I've had the mechanism get out of sync with the switcheson my '97 A6Q. Just popped the cover and tinkered with it to get it back on track.

Try fully closing the roof manually using hex tool. Once closed set switch to closed position.
may need to turn off car and restart. Try using it. My 97 was the same after I replaced battery.
After I closed it manually and set the switch to closed position It worked Ok again.