Why is the “Primary FQDN” Error generated by the SCCM 2012 Prerequisite Checker?

When I run the ConfigMgr 2012 Prerequisite Checker it is failing on the Primary FQDN prerequisite with the following text:

Configuration Manager only supports the use of primary FQDN’s, where the DNS hostname (first label in the FQDN) matches the NetBIOS hostname of the computer. The FQDN provided for this site system does not meet this requirement and cannot be used. Correct the FQDN and try again.

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