Window Regulator Alignment

Hi all
So, the dealers replaced the passenger side window regulator a few months back as it had completey failed and the window dropped on one side. (on the same day i picked the car up from them to get a bad water leak fixed...)
For the first time I attempted to drop the window all the way but notice it stops before it disappears into the door as the drivers side does.
It sits slightly above the top of the door trim.
Have they fitted it wrong or does it need some kind of reset?
I've tried the one where you keep the button pressed but that hasn't helped. The auto close still works anyway.
It seems like it dosen't always stop at the same posistion either, i haven't messed about with it as don't want to make worse if it goes that way.
Closes up OK though.
Cheers