Hi Ollie.
Do you have an FBH on your car as sometimes these can also play tricks with the car if they are faulty, if so try unplugging it, but it sounds like that even though you think the water had not risen high enough in the plenum it could have been sloshing around and splashing up to it when driving around.
Personally even with Jules leaf guard inserted or any other form of leaf protector i still check and rod plenums through the spy hole mod on a weekly basis.
I do this when i do my weekly weekend checks on tyres pressures, and all fluid levels, light checks etc it only takes about an 30minutes or an hour out of your Sunday morning
