vandread - 7:38 am on Jun 12, 2010 (gmt 0)
Thanks, they were singular and plural forms of my trophy KW that were generated by an SEO Plugin. I really don't know if that was the problem, but felt compelled because it was over-optimization, and a blatantly obvious SEO tactic. All my internal linking will now be done manually with some careful thought.
I do however suspect that it was an indexing thing because G is giving far to much weight to my homepage. It is returning the homepage for the SERP ranking for many KWs, rather than the actual individual page. The pages are still indexed, I think G is still sorting itself out.
Interesting. It seems as if I'm in the same boat as you. I also noticed that my HP is ranking for new entries that I write in my blog and not the article itself.
I'm also using an internal keyword tool but not to link to my HP but to inner pages if keywords match. I might be inclined to turn it off for a few days to see what happens.
I'm just not sure of the possible negative consequences this could have.