As a precaution for others to consider when they cringe at the costs involved:
1 . Drill at least one drain hole in the floor close to the immobilizer box .Make sure you locate the hole so you don't drill anything else !
2. Consider using a rubbermaid type tub for the immobilizer, a ziplock bag or one of the pro made waterproof boxes mentioned in Search.
3. Make sure there are screens over all the drain holes or they will plug up again and again & .......You can buy pro ones or make your own.
And if you have just incurred the expense of repairing this problem, all the items above may be attractive ? Part number 987 561 487 00. Could not find them on Pelican but Sunset and ECS have them
http://www.ecudoctors.com/porsche-996-boxster-waterproof-immobilizer-case-enclosure.html
http://forums.pelicanparts.com/boxster-cayman-forum/819818-new-idea-porsche-boxster-immobilizer-clu-water-proof-case.html