As far as I know, all electric window operations are handled by the general module and relay module, two black boxes under the back seat. The general module does the thinking for the windows/interior lights/wipers, and the relay module is just a bunch of relays for the higher current circuits. You have to remove the black plastic cover (3-4 screws) to see them.
I've never heard of this comfort relay, you sure you don't mean the relay module?