If there's a click, then the motor is just struggling to move the window.
Try the door slam trick -- open and slam the doors (not too hard) and this should jolt the drive and the motor should be able to open and close the rear windows.
Anyway, I'm not mechanically inclined at all, and I've had troubles with rear windows before. My guess is that it's something mechanical and not electrical (hence the click), and that it started to happen after the battery change being coincidental.