Regarding the Gedcom file, all gedcom files are exported in their entirety. I see that you have many trees on your family site. Is it possible that you sent them the incorrect tree.
Regarding the pop-up in Family Tree Builder, I think this is because you have an older version of Family Tree Builder installed on your computer.
Can you please try to install the newest version from our site. You do not have to uninstall the version that you currently have, and you will not lose any of your information. This should fix the problem.