All around Problems (Windows and FOB light of death)

[Santent]

So, i got the famous FOB keylight on the instrument panel when i was trying to leave for work 2 weeks ago. BAM.. car wont start, steering wheel wont unlock. Had it towed to dealership. It took them 10 days to fix it. Day 7 they had an IT "specialist" come in to take a look at it. I believe they replaced the BCM and had some trouble troubleshooting the software. They finally got it fixed after 10 days. Now, i see another problem after having it back.

The Passenger side window will not roll back up after opening and closing the door. Everytime the door is opened it will lower slightly (like it always does), but after closing the door it will not roll up. The only way to raise the window back up is to either start the car or put it in accessory and manually do it myself. Did something go wrong with the software or installation? How did they screw this up? I noticed the window down when i picked my car up but thought they must of forgot to roll it back up all the way. They also didnt reset my clock. Such lazy bums. How should i approach this with the service department, im already pissed it took so long to fix my car (they also replaced my battery for 94 bucks without asking me, the only thing that wasnt covered in the warranty). Any input is appreciated, thanks

**EDIT** Solution found on multiple threads, fail on my part. Love you guys