I think I figured it out. I disabled Active Scanning, scheduled to scan every hour. Deleted all computers from the database. The second doamin listed is gone and so are the duplicates.
It appears that one computer has the domain in ALL CAPS while the other is in all lower case. I nthe screen shot below there are two domains with the same name (I have renamed them "domain" to protect the idenity). Computer listed in the second (lower count) are also in the first (higher count). When running a report the duplicates are listed in the report.