I had the same problem when I had my exhaust and intake done. There is something in the manual abut fixing it, that's where I found how to fix it.

start here!
http://www.the370z.com/audio-video/8...-installs.html

Thanks for the this thread guys. I had the same exact problem from disconnecting the negative battery cable.
Here are the directions again: *indicates re-wording.

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. *Push* 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.

If the window will still not close automatically, follow the same procedure but start by closing the window, then keep the button held up for 15 seconds. Repeat for both windows.

Worked flawlessly after I had the door disassembled to add a component speaker.

Both this have helped me when i installed my intake and cbe.

I had the same problem installing my CBE. The steps didn't work so I let the dealer put it on the diagnostic & they fixed it in 10 minutes.