It sounds like you used the User Level Security Wizard--on the first screen it asks you if you want to create a new workgroup information file (yes). On the second screen it asks if you want to make this the default workgroup information file or if you want to make a shortcut to open your security enhanced database (you want to create a shortcut). Did you by chance select "I want to make this my default workgroup information file"? Access comes with a standard workgroup information file that it uses to logon any time access is started (although the logon is not seen if the logon name is admin with no password as is default) and it sounds like you replaced it by accident.
The fix is not really hard, but sort of in depth, so let me know if I'm on the right track and I'll write more...