Occasionally jump starting can throw the system out of sync. However a low battery can cause the immobiliser and alarm to play up as well. I would suggest giving your battery a proper overnight charge and trying again first to see what happens.
Having thought about it, I can't see how it is the key fob that requires re-programming because I have an alarm fitted that has a seperate key fob, that also doesn't lock or unlock the car. My guess is that the central locking system has gone mad?