I experienced this in the car wash just about an hour ago, it wasn't a lot of water but it appears to infiltrate above my head. Timing was perfect I slid open the cover to watch it go over and BOOM, right in the head. I just checked and my passenger side a-pillar and floor are wet so I am guessing the front passenger drain at least is clogged or very slow. I opened the sun/moonroof all the way and nothing was sitting in the top nor does it look like water has sat for any period.
As a Highlander owner as well (and for future readers), one thing on the rear drains. If you are clearing without disassembling do not use compressed air on the rear drains. It could cause the tube to come lose at the upper drain and then you'll have a real mess in the future. I think 9/10 times it's just the fronts clogged anyway, but beware with the rears.