Thank you for your post.
I don't have immediate access to a Windows 7 computer, but I was unable to replicate the problem on a Windows XP (SP3) machine with FileMaker Pro 11v2. This is what I did...
I created a database file, local.fp7, with two tables: local and local2. I related them by a text field "ID".
I created a second database file, external.fp7, and added the text field "ID". I added local and local2 to the relationship graph and related them all by "ID". In the export dialog box, I include the fields from local and local2, and I am successful with the export.
Do you have access to another Windows machine not running Windows 7? Or, can you provide more detail in your instructions so I can try to replicate the problem easier when I do have access to a Windows 7 machine?