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Boxster 2.5 windows and roof not working after new battery

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Hello...I really really hope someone can help as I'm going crazy!Got my Boxster 1999 back on the road, replaced the battery and now I have other issues. The first new battery I had fitted was faulty and as we were driving, the alarm sounded and the windows went down before the car completely stopped.We called out the AA who diagnosed a faulty battery, had it replaced and the car is working well, will drive but the windows are stuck in a down position and will not move! I've tried resetting them but nothing, the roof will not move either and the central locking remote will not work either.The AA man has suggested its the immobiliser but the car starts so I just don't know what to do!!No one has posted this kind of issue before so hoping someone may be able to help!Thank you!

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Start by checking to see if there is any moisture or water under the driver's seat, where the immobilizer is located. If your convertible top drains are clogged and the car sat in the rain or was washed, the water will end up under the seat.

Then check the fuse located on the back of the immobilizer, as suggested by Electrict. You can access the immobilizer by removing the four bolts that hold down the seat rails and just tilting the seat back. That will give you enough access to get at the immobilizer and you won't set off the airbag light (which would happen if you take out and disconnect the connectors under the seat).

For the convertible top, check the fuses located at B6 (power to the convertible top double relay) and D3(power to the convertible top electric motor) in the manner suggested by Loren.

Here is a photo of the where the B6 and D3 fuses are located:


Here is a photo of the immobilizer, showing the screw you must turn to remove it and access the 15amp fuse (rotate that screw 1/4 turn counterclockwise to release it):


The fuse is located on the back of the unit, in between the two connectors.

Regards, Maurice.

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Morning everyone,Thank you all so much,Exact model; 1999, Boxster 2.5L, 68k. It's a UK model, right hand drive and lives in England.The fuses have been checked, as have the relays, I will inspect the immobiliser box this morning.There hasn't been any water in the car at all so it is all very dry but will definitely look. What seemed to cause this problem was the dead battery. Everything worked normally, the windows and the roof until the battery died on us as we were driving, just before it completely died the alarm went off and the windows both simultaneously rolled down. The AA man checked both the alternator and the battery and found it was a faulty battery not holding charge. As this battery was brand new it was exchanged for the exact same battery and replaced.Following the replacement the windows did not roll up. I can hear them clicking as I press the switches both up and down but nothing is happening. The AA man it was a security feature kicking in as the car thought someone was disconnecting the battery to try and steal it hence the alarm sounding and the windows going down. It seems to be a security issue but if the immobiliser has kicked in then why does it allow me to drive it!Getting really upset now as its freezing cold and pouring with rain!

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