Boxster 1999 problems after new battery

[T9SSA]

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!