Try rolling the window down, and then holding the button down for 5 seconds, then immediately go up with it. If it closes like that, after it closes hold the button for another 5 seconds. That should recalibrate the windows. If it doesn't go up then something else is wrong, possibly in the smart junction box? But I'm not sure.
That may or may not help, both my windows would auto-down the other day but not auto-up and I had to do that to recalibrate them.