This happens to me, and it's soooooooooo annoying! Grrr! Goes over ur headunit if u brake too hard too! :O
I did some serious looking at mine, with a jug of water...pouring it on the roof and seeing where it went in... Hmm, I still couldn't find out if it was the aerial or sunroof... Grrr! But yea... immobiliser electrics in there... as long as soonroof switch and maplight... not the kinda stuff I want getting wet!
Dunno if this is related either... but sometimes my IR immobiliser reciever stops working, I have to open the car manually with the key, and then Yank out the reciever, and give it a good cleaning with my hands... then pop it back in and it will work... I think it's the condensation from the leaking water, builds up inside the reciever plastic-cover and blocks the signal.
*sigh*
-Akira