Turn ON the ignition, with the engine OFF, using a master Pass-Key III key (black).
Observe the security telltale (security light on the dash), after approximately 10 minutes the telltale will turn off.
Turn OFF the ignition, and wait 5 seconds .
Repeat step 1 through step 3 two more times, for a total of 3 cycles or 30 minutes.

IMPORTANT: The vehicle learns the key information and/or passwords on the ignition switch transition from OFF to CRANK. You must turn the ignition OFF before attempting to start the vehicle.

Start the vehicle (the vehicle has now learned the key and password information).
Clear any DTCs using the scan tool.

IMPORTANT:

Additional master theft deterrent controller keys (black) or valet keys (gray) may be added (up to 10 keys) using this procedure when there is an available learned master theft deterrent controller key (black).
This procedure adds keys only. This procedure does not erase previously learned keys.
The keys to be learned must duplicate the mechanical cut of the current key.
If more than one valet key (gray) is to be learned, each valet key must be immediately preceded by a learned master theft deterrent controller key (black).

With a previously learned master theft deterrent controller key (black), turn ON the ignition, with the engine OFF.
Turn OFF the ignition and remove the key.
Within 10 seconds , insert the key to be learned (either black or gray) and turn ON the ignition, with the engine OFF. The vehicle has now learned the new key(s).

Sunroof leaks and the windows/door locks not working are covered here http://www.pontiacbonnevilleclub.com/forum/2000-2005-other-than-gxp/topic25362.html
Door leaks are not uncommon, either and there's coverage in the linked section of those, too.
When you know there is one leak, you'd first suspect corroded connections beneath the driver's seat as the culprit for the door lock/window issues.

Having just adjusted my sunroof to sit flush, dropped the headliner to see if the tubes were still connected there and reconnected the disconnected front sunroof drain tubes behind the 2 kickpanels, I can tell you that I discovered more leak issues:
1) The water channel on the roof, above the doors was also leaking, There are drainage tubes within these channels and the leaks were behind the tubes, where the roof is welded on.
2) 3 of the 4 drainage ports on the sunroof itself were blocked by debris buildup.
3) The rear window had a blob of sealant along the top where someone apparently (unsuccessfully) attempted to seal a leak.
4) The passenger's front door water deflector was leaking.

The point is, there may be multiple points of entry for the water.
My carpet was never wet on the surface but the only place where the underside was dry was in the driver's seat area.
The only way to know it was sopping wet on the foam underside was to remove the rear seat and door trim to pull up the carpet and check.
After removing the front passenger seat, I discovered it was wet there , too.

You more than likely have corrosion under the driver's seat where the wires that control the passenger windows are spliced together. The corrosion likely happened from water getting under the carpet and sitting.