I had the same problem and it drove me mad trying to find the problem.
Following on from richhazel's reply, chances are the water is building up in the scuttle (the area below the windscreen where your wiper motor sits). If the drainage holes on either side are blocked the water will rise to a level until it finds some way of working it's way into the cabin. Even though the drainage holes appear to be clear as you say, bear in mind the scuttle area is not 100% watertight so the slightest gap will be enough for the water to escape. It will run down these channels *under* the front carpets where it then gathers in a pool in the rear, soaking it from the underside, which is why the front carpets and the mat on top in the rear stays dry. Clever bit of design!
Peel back your front carpets and you'll see these channels. Be warned - it may smell! Recheck your door seals and make sure the door drainage holes on the bottom of the doors are clear, but I'd bet that the main culprit is the scuttle. I've since sprayed and sealed my scuttle so it shouldn't reoccur. It's a good idea to check the drainage points regularly though, especially in winter with leafs and cr*p flying about. Hope this helps.