Hi, aforementioned boyfriend here,
To answer a few questions and clarify a few things:
Battery was brand new last year, and I didn't actually disconnect the immobiliser, just the sunroof switch (which had shorted and was fizzing) and the cabin light cluster. I do reckon the IR reciever for the immobiliser got wet though.
light does double as the immobiliser fault warning light, the manual for the car describes exactly the current scenario (light only flashes at idle or low revvs), so i guess the immobiliser has shorted somewhere, i assume when it got wet.
I had thought it might be because the battery was drained completely, but in my experience this only really damages the cells after continuous charge and discharge.
So since the battery is so new, I had been thinking it was some kind or short circuit that has been draining it, caused by the leak, is this feasible? either way i guess we need some kind of car electrician to sort out the flashing light/immobiliser issue.