whatson - Several thoughts...
Since these are templated and I assume represent roughly the same design philosophy, I'd look at factors that occur across all of your pages/sites.... a)
It might be that html text containing company name does not occur on the homepage... or that there's insufficient text. I've seen this happen more than I would expect. b)
It might be improper canonicalization... particularly of the index.html variety... ie... http://www.example.com/index.html
...is a canonicalization issue that would split inbound link juice particularly to the home page. c)
Possibly too many exact match anchor text links pointing to the homepage, causing Google to give the page an algorithmic penalty.
Additional questions that might help us identify the problem...
- Are all of the pages roughly the same age?
- Inbound linking... was it done independently for each site, or do the sites share a common pattern... possibly even common inbound link sources?
- Do the sites interlink?
- Are the sites in the same market area?
You've got to look at the situation closely enough to give us more information (without getting into specific search terms or market areas).
A related thread worth checking.... Why Do Some Homepages Get Buried? http://www.webmasterworld.com/google/4410350.htm
I also suggest site search, as this is a problem that's been going on for years.