My central locking has ceased to lock the boot. It locks and unlocks the 4 doors fine but neither locks nor unlocks the boot.

HOWEVER, when locking the boot with the key via the boot's own lock, oddly, it will lock/unlock the boot as well as the doors.

What could be causing this?

Hard to say, could be the lock position sensor. On the lock cylinder (doors with an external key lock) like driver , pass and rear boot , on the locking cylinder , on the inside there is a sensor that fits around the locking cylinder and reads the position of it. It may already be reading its in a locked position so it does not lock the boot when yu lock the other doors. But when yu go to the Boot to manually lock and unlock when yu lock , or unlock it is locking and unlocking all the doors via the central locking actuator. When yu turn to lock it pushes on the lock rod frum the actuator and locks/unlocks the dor. Also the actuator can just be bad. In cases it may most likely be the locking actuator.