Certificate showing up as invalid even though the domain name matches

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http://serverfault.com – We just bought a certificate for files.website.com. We have installed it to the file transfer software we are using (Globalscape EFT) but are still getting an error message saying "The site's security certificate is not trusted!" I go to view the certificate from the browser and the domain name matches exactly with the name in the certificate. What am I missing here? Thanks for the help. (HowTos)