dvduval - 7:32 pm on Jun 14, 2010 (gmt 0)
If you have strong anchor text and have not changed the title tag, and the main difference is you have one H1 tag instead of five, that makes me wonder if this is a case of google caffeine quickly noticing there have been changes, but then backlogging the consideration of the changes you made, or worse, applying a sandbox like effect to websites that have undergone significant changes.
I have been having a similar problem. I almost feel like making improvements to your site (even those recommended by google or its staff) can have short term negative effects. I am just staying calm and thinking wishfully that because I have made improvements that google would 100% score better, I will soon see the benefits of my work. But I must say it is unfortunate to see short term setbacks, though this is nothing new to me.
In closing I do feel there is a sandbox affect applied when there are significant changes to a site and would love to get some feedback on how you agree or disagree.