Had a similar problem with my 05 as well, just too many leafs collected under the cowl grill and blocked any water from draining out, and it eventually started leaking through the intake vent contained in that section and spilled tons and tons of water in the passenger footwell, and it didn't help it was still raining at that time. Literally had a pool in my car, and it was covering a lot of the wiring behind that kick panel in the passenger side. Shorted a few things out temporarily, lights wouldn't turn off, windows wouldn't work, radio wouldn't shut off when I opened the door, brake lights and indicator lights in the back stopped working, and the middle of the right brake light stayed on constantly. After I dried it it immediately started working again.
Could be similar to your problem plus or minus the water, but can't hurt to check and see if maybe a little drained in and collected enough to short out the wiring temporarily. Or it could be having a Ford moment.