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The only issue I can think of is that this site is one of several sites that each have a listing in the same category in Dmoz. The other sites have since been folded into the main site and the domain names 301ed to the main domain. This means that there are several different listings in Dmoz all pointing to the same site. Could this be what's confusing Google?
I'm at my wits end because I have followed the correct procedure as posted on Google's site. The client will drop me if this continues. Any of you gurus have any ideas?
secondary domains in the SERPs
count_zer0 can you expand on your idea of secondary domains?
e.g. another domain pointing to the same IP?
Sub-domains -- e.g. sub1.domain.com sub2.domain.com
Completely different domains the secondary re-directing to the primary
I'm not sure what you are defining as "secondary domains".