I recently bought an IS300 SportCross and the lady who owned it told me the windscreen had been replaced and since then the alarm goes off whenever it rains. I discovered the front passenger door had a faulty sensor so i mended that, but after a night of heavy rain I woke up to lit headlights and rear lights. When I inserted the key in the ignition the lights went off, but came on again around 30 seconds later. After an hour or so the car had dried up and the lights turned off on their own.
I found and read this thread before diving under the dash to have a look at the Theft warning ECU. It looked perfectly fine on the inside though.
The rain started pouring down again and I could see the occasional drop of water falling on top of the right side fuse box. Upon closer inspection I noticed some of the connectors looked pretty corroded and nasty. I decided to remove the fuse box, disassemble it and clean it thoroughly.
This pin had almost corroded right off
The main problem is of course the leak around the windscreen, but I bet this clean didn't hurt. I just thought I'd post this to add to the knowledge if anyone else has the same problem in the future.