The external database have two different kind of update sequences.
I think this is the same thing than what is described in the user guide:
Another issue here might be that changing permissions, say, by named access control list which has only users, not user groups, will cause a background task generation to queue up to be applied in it's turn. While this is running, no other background tasks are done. If the document vault is large, this may take quite a bit of time until the task finishes.
You could check the M-Files Admin tool for the backgroud tasks, if the operation would be still going on.
Overall, it's advisable to set users to user groups, then add these user groups to access control lists. That way things go way more smoother.
I may have also partially misunderstood teh concern here, but these are at least some factors that could cause latency to the permission change of existing objects.