Class Permissions

Did you select "Change and Activate Objects' Permissions" when you applied your settings?

Yes, i selected that

Im using File Sources to import the document if that makes a difference?

I just ran a quick test on a demo-vault. Taking the vault off-line and back online did the trick for me.

Apparently changing permissions is a background task that may take a little while to complete. Perhaps if you give it enough time it will do the job without taking the vault offline.

It works, sorry was being too impatient and not giving it enough time.

Yes, permission recalculation is a background task nowadays. You can monitor these tasks in M-Files Admin: Monitoring Background Tasks