We have taken a slightly different tact in looking at the problem and are now assuming that the indexing issue is internal to the websites. Google has always said there is
almost nothing another webmaster can do to hurt your site ...
6. EMPTY CATEGORIES
We are seeing many websites that have a huge number of empty categories .... if you don't have listings on a page you should nofollow these empty pages. Like charities are ever going to bid for position.
7. DUPLICATE CONTENT
Now here is an issue that looks like it is causing our problem .... large numbers of sites are showing duplicate content AND having indexing problems. Also many sites that are not having issues show very little duplication in content.
At first glance I was thrown off due to several sites having a large amount of duplicate text but no problems. However after checking again we are seeing that this is mostly template duplication --- must not draw a penalty?
I strongly suggest you run your entire sites through Copyscape --- it now looks like we created this problem ourselves!!!! SO MUCH TIME WASTED LISTENING TO SEO EXPERTS, GOOGLE BASHERS AND DIRECTORY HATERS!!!!