You will need to do a save and reload for the separate zones to be registered. It’s a known bug.
As @Rubble says, but could be that a S&R doesn’t work then you have to delete the security station(s) and try again. Also keep in mind that if you removed a stand that the ‘old’ security zone still exists, also a known bug.
Lets add (again), that all objects that you delete, that have a secure zone associated with them, will keep the zoning; even Terminal Blocks.
Did you try to disable and then re-enable security stations?