Security is made up of Accounts and their Privilege Sets.
Generally you will have an Account for the developer with [Full Access]
By default there are 2 other Privilege Sets including [Data Entry Only] and another which is [Read Only Access]... but you can create more and assign them to your user accounts.
I don't think you can delete the default sets...
In addition, there are setting within those Privilege Sets about what sort of access you are going to allow those users... like PHP, XML, WebDirect, FMNet etc
I suspect that one of the databases has some of these privileges for the user account you log on with set differently... or maybe you have locked yourself out by deleting an account with [Full Access] or similar.
It all gest pretty tricky and I suggest that if you can't make sense of the Help and documentation, that you pull in an expert to help you set up what you require.
To fix things you may have to take the databases off the server and open them directly with FMP to fix the privileges before you return the file to the server.