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With the power on, try to open and close each window seperately using the controls on each door. This tends to happen when you unhook the battery cable.
Each window switch will be blinking. simply hold down the down the switch for 5 seconds and up for 5 seconds. Repeat for all then test at the drivers controls. simply fix.
I did the same thing a few years back. I had my friend paint and install the GFX kit on my IS250.
I didn't know about the reset procedure back then so I called him and said.... what did you do to my car, I had you paint it and now my windows don't work????
End result, me feeling like an idiot.