The first things I'd check are:
- Are both files hosted together, were uploaded to the server together, and both have the extended priv for fmwebdirect enabled for the correct priv sets and accounts so they can both be read via webdirect?
- Do the account credentials match between the files?
- Does the value list in the external file use a dynamic or custom-value list to generate content?
If dynamic, such as based on a field's content, check the context for that data.
If dynamic based on related records, the context of a layout's base TO is required to populate it, so it may not populate into another file properly.
- Is the external file referenced in the relationship graph so it will be opened automatically as needed?
That's a start.
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Also, make sure that the matching credentials in the referenced file specifically have WebDirect permissions enabled for the user account you are logging in with. To elaborate on #2 in Stephen's list above.