I am surprised that didn't cause a dead short, just goes to show that a little knowledge is dangerous!

I would start with the basics I.E finding out what the different wires do for the windows and then work from there, the wiring sounds very dangerous, normally there is no connection between the interior light switch and the windows, only thing I can think is does it/has it had a full closure alarm fitted?

Look at the window switches and see if they have had additional wires spliced in.

Martin