Window problems
 

I recently had to replace my alternator and battery. I unhooked the battery first and then replaced the alternator then just went in reverse, hooking up the battery last. Now I am having issues with the windows not rolling up proper after I get out of the car. I have a 2005 V6 4.0L and the windows are supposed to automatically roll up that last bit when you exit the car and they wont do it. Any Suggestions? I thought about resetting the computer but I have a performance chip installed and am worried about how resetting the computer would effect the chip.