2005 Renault Scenic central locking

clutch and gearbox broke which resulted in the battery being disconnected for two weeks while the gearbox went to be repaired. since we have had it back we can't get the central locking to work. when the lock is pressed on the remote it will flash and shut the windows but won't lock the doors. the boot lock was not working either and we have had a new one. the boot lock will open and close with the remote. any ideas please would be fantastic.