Two Most Likely Places
First, the front seam of the tip-up. Mine actually seems to do a much better job of keeping water out when it's moving thru the air rather than sitting on the ground. Solution is to tape the seam (painter's tape will work) just before you put the cover on.
Second place is the back edge of the bubble. Even if you've sealed the edges, you're likely channeling water to the bottom of the bow - it's going to get in somewhere. Again, tape it.
The Bruce covers are great, but they're not completely waterproof. Even gore-tex leaks if the water is left to stand on it. Just like foul weather gear for sailing, the only thing completely waterproof is rubber; but it's usually to hot or too heavy.
Finally, don't forget the NACA vents. I'm usually rewarded once a year with an in-cockpit spray shower if the plane is sitting out in the rain and I've forgotten to cover the vents.
Terry, CFI
RV9A N323TP