In my case, the little flapper valves in the drains block off most ofthe drain hole, but there is still a little gap where you can see light. I would derscribe mine the same way you describe yours. I have looked at mine closely, and they do not appear to be malformed or defectiive, I just think that's the way they are.
The flapper valve appears to be intended to prevent a lot of dust and water spray from flowing up through the drain, but I'm sure it is not perfect. The problem is that the valve has to be free-flowing enough to allow all water inside to flow out, even if it is a few drips. The issue here is that there is no water pressure behind this draining water. That means that the valve has to be very flexible and easy to open.
The downside to that is that it is easy to open for water coming the other way. Given a hard enough rain, and driving through some puddles (which is inevitable in such a heavy rain) I have no problem believing that water could splash up hard enough to come back up the drains.
I suppose that it would be possible to design a valve that would prevent this water from splashing up, but then that would limit the maximum draining flow rate through the valve, or require a certain amount of water pressure to allow drainage (meaning that there would have to be significant water accumulation in the bed before it would drain.)
As it is, I'm guessing that the current design is a compromise balancing the conflcting requirements of flow capacity, low drain pressure, and limited back-flow.
I'm guessing you hit so much water, that you passed the back flow limit. It's probably a fluke, and I wouldn't worry too much about it happening in the future, unless driving in that much rain is a common occurance for you.
Of course, that's easy for me to say, since it wasn't
my gear that got wet. I'm sure you're looking at it a bit differently right now.
-- SS