I got a cowl seal from one of the vendors that was supposed to be the greatest thing since sliced bread. It was way too thick and stiff and made the vent stick up above the cowl. I went with the more original style foam seal, although I haven't had my truck out in the rain yet to be sure it doesn't leak.
You might need to look at the lower edge of the vent that contacts the seal to be sure that it's smooth. Also be sure that the drain tube isn't plugged.
