Alright, for some reason I cannot roll down the passenger window from the driver side controls. The control on the passenger side works perfectly, as does the driver side window's control.
The passenger window lock button is not pressed. I have never taken off the door pannels. The only mods I have done to my car that have to do with anything electrical are a subwoofer and a grounding kit. I don't know if disconnecting the battery would have caused this problem.

I'm not sure how long this problem has been going on for, but I just noticed it today. (It may actually be the first time I've tried to roll down the passenger window since purchase in Dec.)

Any ideas how I can fix this, and be able to roll down the passenger window with the driver side controls?

u need to reset your windows

yes it's in the owner's manual. anytime you disconnect the battery, you will have to re-initialize the windows, and the sunroof.

i believe holding the window swtich up (or down, but makes more sense to be up) for about 10 seconds. that should reset them.

yeah, just hold the passenger side switch down for 5 seconds, then pull it up and hold it for 5 seconds. that should take care of it.

there's enough threads about resetting your windows...