I have exactly the same issue but it is just the back driver side door that doesn't recognise it having been opened, there I was last week putting my 3 year old in the back seats with his friend and left keys on seat. The car locked and both of them were locked in the car. After 30mins of the alarm going off and trying to get the door opened I remembered they could use the key fob to unlock it. Luckily they did.
Have you had a response from this yet?
i would take a look at any wiring in the door gaitors to see if they are frayed or broken if all ok then have a look at the central locking module if no joy here then(clutching at straws here)it may well be a software problem if so then its a dealer visit.
there isnt to much info around on the mk3 yet and if it is then its under lock and key where you have to pay to join certain forums.
i dont know if the central locking module is connected to the alarm module but if its anything like the smax then iirc its found under the passenger wheel arch area.
hope that helps a bit.
just a thought on this,if you have the convrs dash,you might be able to set/unset certain items from within the system in it?