This is an old thread but I'm bumping it as someone who recently ran into this problem after heavy rains in Houston. Our driver side rear drain wasn't totally clogged but clogged enough that with the heavy rain the drain overflowed into the passenger cabin on the driver's side, saturating the edges of the panel behind the seats, pooling under the driver's seat as well as soaking the carpet and padding & frying our SmartTop. The latter caused all sorts of strange behavior with our Boxster including the alarm going off and refusing to disarm, an airbag warning light, a system fault message, a soft-top control system fault message, driver's side frunk & trunk switches not working & the spoiler being stuck in the raised position. After drying everything out and uninstalling the SmartTop everything seems fine.
Keep those drains clean! If your dealer is servicing your vehicle then make sure they're clearing the drains. We just recently had ours serviced at the dealer and I find it hard to believe that this drain clogged so quickly.