OP, welcome to the world of marginal convertible top seals. Let me guess - the leaks are at the junction where the top attaches to the A-pillar/Windshield frame? There is a reason why I am an ex-E93 owner. Mine was repurchased under California's Lemon Law after 4 failed repair attempts for leaking (at the same A-pillar/Windshield frame). If you want to see what a real convertible top seal should look like, check out the seal on the new Z4.
BMW NA would rather that you just suck it up and suffer in silence about the top leaks. But if you live in California, there is hope for you. Get 4 failed repair attempts, send a written notice along to the contact address in the warranty booklet and get a good lemon law attorney and you too can be free of the marginal top seal problem.
Good luck in your efforts.
EDIT: I just noticed that the OP is not in California. Bummer. You may have to just suck it up.
Last edited by anE934fun; 10-20-2010 at 07:33 PM.
Reason: See EDIT: