Tiptronic stopped working. 1997 2.5
 

I haven't used the car for a couple of months and it had to sit outside in that time, the drains were blocked and the rain water had filled up under the passenger seat submerging the ecu. I dried that off and the central locking etc are working fine, but could that have any effect on the tiptronic system??
The car drives fine in auto, but does not recognise when manual is selected, the led for "M" does not illuminate on the dash!
Any hints or tips where I should look first would be appreciated!!
Thank you.

Its not likely that the Tiptronic control unit was damaged since its located in the rear trunk (next to the ECU).

I'd start by looking at ALL of the wiring under the seats. The problem you describe sounds like a problem with the transmission multifunction switch . This switch is located on the transmision and is actuated by the gear selection lever cables and tells the Tip controller what gear was selected. Maybe some of the wiring from the multifunction switch runs inside the cabin and was damaged.

If Boxster tips are like Audi/VW's, there is a magnet in the shifter housing that activates the sensor for the tiptronic actuation. The magnet is actually on the plastic "cover" that moves with the lever, when you slide it to the right, it moves the magnet under the sensor and recognizes that it is in tip mode, and moving the lever forward/backward moves the magnet under the upshift/downshift sensor. I've seen the magnets fall out of Audi/VW housings, and I've super glued several of them back into position!