I have a 2006 C6 Coupe having the same door window problem on the passenger's side.
The door had been replaced ..Battery went dead and replaced the battery. The window stopped 3 inches from the top. Repeated tries did not fix the problem. Tried the 3 second method to initialize to no avail. The window will go down and up but stop 3 inches from the top. When it reaches that point it seems to keep "jumping" back slightly when I hold the up switch.
How can the problem be fixed ?
Thanks if anyone can give me any input.

 

Initializing must be done with both doors closed...this may be why it didn't work. Give that a try...and you might try waiting more like 5 seconds, three may not be quite enough.

 

If all else fails, you might try disconnecting the negative cable for a few minutes and then re-attach and try again. Good luck.

 

Thanks, Will try that and see what happens......

 

I'm sure I had both doors closed but will try that again.....Thanks

 

Just to clarify...if this started happening right after the door was replaced, then it's probably a mechanical problem, but if things worked fine after the door was replaced and then the problems started right after the battery died, then it is most likely an indexing problem. Because of the way the window indexes up the last half inch when the door is closed, the computer has to be aware of the window position at all times, which is why the indexing has to be done after the computer loses power. It can't index the window properly if it does not know the present window position.

 

I'm suspicious of a mechanical issue after the door replacement but hopefully it isn't.

If the previous suggestions don't do it, try doing a DOWN and UP index. Same procedure for the Down as the Up, ie: push the Down switch and hold 3 seconds after it reaches the full down position...release the switch and push and hold it down for another 3 seconds and release. Then do the same process for Up.

 

Problem Solved !!!
This is the way it finally cleared the problem went for anyone that ever has that problem.
First I closed both doors & lowered both windows at the same time and raised them again at the same time...Did this several times and held the switch for me than 3 seconds.
Did NOT fix the problem of the 3 inch opening on the pass. door.
Second I lowered both windows and disconnected the negative battery post and left the cable off for 5 min. Then re connected the negative post and went inside and closed both doors. Tried to raise both windows.....A strange thing happened in that the driver's door window went up but the passenger door window did not move. I tried to lower and raise both windows several tines but to no avail. The pass.door did not budge and was stopped in the completely open position.
I was getting worried that this was an electrical problem ..Not good!..With the driver's window up and pass door window down I decided to give it one more try.
I pulled up the raise switch on the pass side ..nothing.....I kept holding the switch in the up position for 3, 5, 10 + seconds. Suddenly the widow raised to the full close position!!
I was shocked as I was about to give up. I guess it must have been an indexing problem as
you all suggested.........Thank you all.....You have been a lifesaver !!!!

 

That's an indexing method I haven't heard of. I hope there is not a problem with the right window regulator. This is what it looks like. Both of mine have been replaced.