Hi Lewis
When you restore from a FBK the system rebuilds the structure of the database so you can see the users in the NAV side (As those are actually data records) however cannot see them in SQL (As that is structural side)
Couple of options,
You can redo the transfer as a SQL backup, this will bing the structure as well
Capture the users manually onto the new SQL server
or use SQL scripts to transfer the users (This is pretty complicated so don't attempt unless you have someone with SQL scripting skills)
Cheers
Nev