I'm having similar problems, and was surprised to find that water collects underneath the rubbers seal along the entire edge of the top's storage compartment. Just push the rubber a bit, and you'll see a water channel underneath. It looks like this is to drain into the gear wells and then out the drain hole, but ... while driving, inertia tends to slosh the water around inside the TSC (top's storage compartment). With the compartment lid up, you will see thin black plastic "plugs" about an inch in diameter. Water will leak into the trunk through there.
First time I had about an inch of water in the spare tire well (was driving). Second time I had the passenger's gear well fill up, but no water in the trunk (wasn't driving). The drainage design puzzles me, but I haven't had time to took very closely (it's raining right now). In the meanwhile I've been using a car cover when it rains, and so far both trunk and TSC have been dry.