Hi Ace,
While some people call the IMSB issues the Achilles heal of the 1997-2008 Boxster, a potential high ankle sprain for the car is the wet immobilizer. There is much information out on the inter-web about this (try the 986forum), and I am not an expert in this.
But the usual culprit is clogged drains. There are some in the drip trays under where the top stows, and some in the front under the cowl. A hole torn in the drip tray could be the problem as well, as well as leaky door membranes. I'd guess you have a leak in the driver's side rear drain. Check that first. Clean any obvious leaf or pine needle debris, and blow some air down the tube. Then pour a little water into the drain. You should see it dripping through to the ground in front of the rear tire. If not, you may have to try to "roto-rooter" the drain tube. Once clear, may people buy screens to cover the drain holes. Suncoast Porsche Parts has them.
Once you've fixed the leak you'll need to pull the seat (disconnect the negative terminal of the batter first, so you don't throw an airbag light) and dry out the water. I believe the carpets are especially difficult to dry completely due to the type of foam backing used and will need to be removed from the car to be heat/air dried. Then you'll have to pull and open of the immobilizer itself to thoroughly dry it an inspect for corrosion. I hear light corrosion can be cleaned with isopropyl alcohol, but it is possible the unit is kaput. Then you will be looking at a significant expense to properly replace, as I believe the unit is coded to the car and you can just plop a used one in there.
Good luck!