My 2008 has it too.

 

What Ford had done until sometime in 2006 was turn off the auto down for a 1/2 inch when you opened the door. It was put back in sometime in 2006 and has been a 'feature' ever since.

There were issues with it at first, something like not going back up, or when it iced up it couldn't open... those sorts of things. You could get it turned back on at the dealership with a request. Apparently Ford figured it out and left it on.

It's more an issue with closing the door than opening it, though. If the windows are all the way up, they can't get closed into the channel of the weather strip. Has to be a little down to get the door to close, and then the windows pops up into the channel.

Reminiscent of old 64+ Lincoln convertible suicide doors. The back door glass HAD to roll down just a touch to open and close the door, or it would rip out the weatherstrip that rode against the front glass. It was rather unique at the time.