Found this out today - it's listed in the owners manual but I thought I'd mention it here for folks in case they scratch their heads about this later on like I did (this may have already been mentioned, but rendundancy is okay). 
After you disconnect the battery (or if it goes dead), the auto-up feature of the front windows will be disabled. I have no idea why...but the manual states this as normal and talks about how to reset it.
I thought it had something to do with my Jet chip (compromised wire during the reinstall of the ECM, glitch, etc).
Easy to fix - with both windows up, all you have to do is this : hold each window switch up for 1 second with the window in the fully closed position. Then, deploy it to the full open position. After that, the auto up feature will be re-enabled.
Guess there wasn't an open variable to save that state with the power disconnected...wonder how many people will never figure this out after a battery change or disconnect (I'm always slightly amused at how many folks forget that they have an owners manual!
)
After you disconnect the battery (or if it goes dead), the auto-up feature of the front windows will be disabled. I have no idea why...but the manual states this as normal and talks about how to reset it.
I thought it had something to do with my Jet chip (compromised wire during the reinstall of the ECM, glitch, etc).
Easy to fix - with both windows up, all you have to do is this : hold each window switch up for 1 second with the window in the fully closed position. Then, deploy it to the full open position. After that, the auto up feature will be re-enabled.
Guess there wasn't an open variable to save that state with the power disconnected...wonder how many people will never figure this out after a battery change or disconnect (I'm always slightly amused at how many folks forget that they have an owners manual!