A couple of issues that might be affecting license count include a location linked twice or permissions are not given for the user to see the all the cameras.
The first possible issue is that an archive location is linked to different locations. This can be recognized easily by the same list of cameras showing for two separate locations. (This can also been determined by looking for the duplicate IPAddresses/DNS Names in the ipAddress field in the dbo.tblserver table in the management database (ESM5_2_Central).)
Another possible issue may be that the user does not have proper group permissions to see all the cameras. This was common in older builds of ESM (V5.3 and before) as you previously had to give permissions to the cameras in groups each time you added another camera. In order to check this, you can sign into the ESM Admin interface and go to the group that your current user is signed in as. Make sure each camera in the tree has a check mark giving permissions to that user.