Thank you for your post.
Every file hosted by FileMaker Server needs a local "Full Access" username and password. Are you able to access the file(s) using the local username and password? If so, then your External accounts are not being accessed properly. If you cannot open a file using the local username and password, then I would uninstall and reinstall FileMaker Server.
Question for everyone: Has anybody used FileMaker Server running Windows Server 2003 on a Mac?
The FMPS runs on a Mac.
The Active Directory is handled by Windows 2003 SBS.