I clicked on the settings button and also configured the LDAP service (unsure if this works) to login with the account and password that has [Full Access] to the file, but still I have restricted access and unable to view multiple tables, edit layouts, etc.
First off: that has nothing to do with authentication. Those LDAP settings (and its siblings on the FMS admin console) are only for *finding* the FMS in a segmented network. They play no role in the authentication process whatsowever.
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In the FM file, check in the menu File > Options
to see if the file is setup to auto-login. Chances are that it is. Toggle that off, it is not secure that way.
Probably the reason that you were prompted for creds in WebDirect even with that setting toggled on is that the priv set that is assocated with the auto-login account did not have the webdirect extended privilege enabled.
Another option is that the credentials for accessing it through FileMaker Pro have been saved to your Keychain, so you are not being prompted for it.