There's a few settings in the GM related to window settings. Not entirely sure what all of them mean. but for example the windows by default will not work if the doors are open/opened, will not work as soon as the ignition is turned off, and the passenger window is not enabled for one-touch raising.
All of these can be coded back in, so on my car now my windows will work with the ignition off (for one minute), and can be raised/lowered with the door open.
I assumed this is the issue that the poster was having, hence I mentioned there are code settings for it that may explain it.