Rich, it sounds maybe like the bulb seal is not quite making full contact with the top up? I can't imagine "pin sized holes" in the bulb seal itself.
If the contact is not good, you need to raise the top just a bit by shortening the cable to that area. Before you start making adjustments, measure the distance between the outriggers that the top rides on when down and the lower edge of the top. Ideally, the four distances should all be equal, but it's likely there is some difference between them. If the area where you see the "holes" is lower, that end needs to be raised.
There is an adjustment procedure in the manual that involves using four equal length 2x4s to support the top and I strongly recommend doing it that way.
Don't raise a low end too much though. You just want to get a good seal contact. If you raise the top too much, you can cause damage to the point were the cable attaches to the top. (I know this from experience.)
- Jack