Most have had problems with windows after the disconnect the battery and then reconnect. Is that what you did? Anyways try this.
WINDOWS NOT WORKING PROPERLY AFTER INSTALL
If the windows do not close automatically
If the power window automatic function (closing
only) does not operate properly, perform the
following procedure to initialize the power
window system.
1. Push the ignition switch to the ON position.
2. Close the door.
3. Open the window completely by operating
the power window switch.
4. Pull the power window switch and hold it to
close the window, and then hold the switch
more than 3 seconds after the window is
closed completely.
5. Release the power window switch. Operate
the window by the automatic function to
confirm the initialization is complete.
6. Perform steps 2 through 5 above for other
windows.
Also check fuse as spearfish25 stated.
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