My drivers side front window goes all the way to the top it seems, but it leaves a 1/2in crack along the pillar next to the driver head rest. Also, I am guessing this might be a clue, when you put the window down about half way down it starts to slide fast then go back to normal speed.

Any ideas on what might be the problem?

 

still under warranty?

 

Yes, if it's under warranty have the dealer look at it.
Otherwise, take the door panel off and check the bolts that hold the window mechanism to the door skin. They are known to loosen and cause problems with the window operation, and in extreme cases the bolts can actually tear through the metal from the torque. You want to catch the problem and correct it before this happens.

 

Unfortunately the car isn't still under the 36k mile warranty... Mulder unfortunately was right... two of the bolts to the door fell out, and the last bolt ripped apart the metal around the hole...

I put the bolts back in with a lockwashers and the one that had destroyed the metal; I put a big metal washer and a lockwasher. I guess this is a temporary fix until it happens again or I come up with a better fix for it.

 

Short of replacing the door itself, there isn't much more you can do. If it's holding together and working properly now you've done all you can. The only other thing I would suggest is to use Loctite on the bolts if you haven't done so, this should prevent things from loosening up again.