I have the same problem, water is getting in at some point. In my case the rear window seal is leaking, also had water coming in around the sunroof although i think i have fixed that one. I think i had water coming into the boot from the fuel filler cap, again that one now sealed. It's just a case of trying to locate the leak, are any of your carpets damp (including the boot) or a mouldy smell in the car?
hope this helps,
Jim.