Check to see if your cowl seal is actually making contact with the body of the Jeep and
is attached tightly to the bottom of the windshield frame.
Sometimes, the cowl seals can shrink some, and they don't actually get compressed between
the Jeep body and the windshield frame, causing a very skinny gap. Because the seal is
attached to the windshield frame, the gap is going to be at the body of the Jeep.
It doesn't have to be a very big gap to let stuff get through. The gap can be small enough
that you might not have seen it when the seal was installed.
When you are driving, there is the full force of the air hitting your Jeep at the windshield, and
that force will drive rain, snow, dirt, you name it, into your Jeep.
I won't tell you how I know this!
If you have a gap you can try three things.
You can try to pivot the windshield frame back just
a bit more to help compress the seal. You have to be careful, as you don't want to pivot
the windshield frame back too far, or the doors for your soft top won't fit against the
windshield frame right.
Another thing you can try is to get some sealant and apply it to the bottom of the cowl
seal, and then when you pivot the windshield frame into place, it will help make better
contact between the Jeep body and windshield frame. The downside to this is that
it becomes permanent, and if you flip the windshield down again, you might tear the
The third thing is that you may need a new cowl seal that is thicker. Some makes
are better than others, and are thicker than others. This is the last resort attempt,
as it expensive.
I hope you figure it out soon, and most of all enjoy your Jeep!!