I have an 08 WK and i just had to replace the battery and now the auto up function of the windows does not work properly. I did what the owners manual said to restore the function but it has not fixed the issue.
basically it says take the window all the way to the top then hold up the window switch for 1 second to reset it.
press auto down and hold it after its down all the way for 3 seconds. And then press up and do the same thing. You should hear a little click. Try that. It may take a couple times but should do it for ya!