So after having a look under the dash, everything appears to be perfectly dry. No sign of moisture anywhere so it must be something under the hood or the ECU itself, but being where the ECU is located, it doesn't make any sense that it would dry up so fast if you run the engine for a minute, and this problem doesn't happen when the car is being driven in the rain..This happens only when the car sits parked in the rain, and it seems to be that a light rain doesn't affect it. Only when it rains hard does the engine act up when you go to start it..I would think that if the ECU were getting wet, it would cause the engine to misfire while driving the car in the rain, but you can drive it all day long in the rain and it's fine..It only happens when it sits parked in the rain..I'm pretty sure this only happens when the engine is cold and it rains..Doesn't have to be real cold, as in 30 degrees, it can be 80 outside and if it rains overnight, it will misfire when you go to start it in the morning..I do not recall this ever happening when I shut the car off (engine hot) when it was raining and got back in 20 minutes later and started it up. If the engine is hot, it's start up and run fine...So whatever it is that's getting wet causing the misfire, has to be cool enough to let moisture form on it..If the engine is hot, it will run just fine...But now I have a problem with the immobilizer..So I have to figure out how to get the immobilizer to recognize the keys again...Immobilizer light flashes no matter what key I use..

I had pretty much the same problem,but with a 2001 Cabrio. I live in North Florida and when it was cool mornings it would not start. So at night I started my car and sprayed lightly with water looking for arcing.
Found it right away my coil is located on the firewall and rain got to it. It had a small crack.
I changed it,15 min job $17 on eBay ,and No more problems. I did have intermittent misfires before and a little loss of power.
No more, runs smooth 2.0 ABA 210,000 dosnt burn a drop of oil, but now have the infamous ticking at cold starts of the valves I believe .
I hope that helps

Heavy rain leaks into footwell...
 

GRBullets your post about the firewall makes sense as I find my footwell is flooded/wet after heavy rain - having just got back to the office at half 6 pm and with work to do as the heavens opens I hope I don't suffer your problems when I try and go home later!

Have you or anyone succeeded in finding the source and stopping the cause of this leak?!