Are you sure the file that you are opening directly is the same file you are linking to as an external data source, not a cloned copy? You can open Manage | External Data Sources to check and see the exact filepath to the linked file.
With the linked file, you may have a relationship involved. (You don't indicate how you are checking for records here, looking at a portal? Finding the file in the Window menu and opening it?) That relationship might be keeping any records in the linked file from being visible to you.
Thanks Phil for your response.
This is very strange. I've recreated the files and now it works. Dohhhh!!!!
Did exactly the same as before - don't get it but at least we're making progress.