If it's an '01 and no one has replaced any parts related to the convertible top, you have the B Version transmissions and set up.
If that's the case, then you do have the correct double relay installed (black square).
That also means that you will
not have the B Pillar microswitch (found under the semi-circular black plastic carpeted panel around the base of the roll bar on the driver's side) and you will not have the black lever microswitch (found on top of the electric motor). Those are in those locations only in the "A Version" set-up and were both moved to INSIDE the driver's side transmission on the "B Version" set-up.
Since you mentioned that your drains were clogged (and you previously mentioned that the windows dropped all the way down), I would check under the driver's seat to see if there is any moisture or water in, under or around the central alarm control unit. If there is any doubt, remove the unit and open it up to check for moisture or corrosion inside. If you catch it early enough, you can dry it with Isopropyl Alcohol and a hair dryer after the alcohol has evaporated. Also check that the 15 Amp fuse at the back of the unit is good. It's located between the two plugs.
Here is how to get access under the seat without setting off the airbag light:
Central Locking System Problem - 986 Series (Boxster, Boxster S) - RennTech.org Forums
You did not lower the top into any electrics because there are no electrical parts that would be affected by a couple inches of water in the convertible top well. You only get those problems once the water migrates under the driver's seat.
If there are no problems with the central alarm control unit, I would definitely isolate the electric motor and check it with an independent 12 volt source.
Regards, Maurice.
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