Trav - 10:19 pm on Jul 8, 2010 (gmt 0)
Some interesting replies here; my feeling is that there's more to the story here. Re-factoring to a CSS-based layout just doesn't cause this in and of itself, at least not on any of the sites I've updated.
I'm using the STRICT doctype (minimal errors upon validation)
I basically stripped the pages down completely and created a CSS-only structure.
You mention there are "minimal" html strict errors. You might want to fix those. Have you noticed any changes in google webmaster tools? Did your css id/classes include your keywords? (over optimization?)
I'd start here- either fix the errors, or use a transitional doctype. Then make sure you've used semantic elements for your content, h1's p's etc. Then make sure you haven't moved a whole bunch of less-important stuff up higher in the source code. Finally, have you taken a look at your robots.txt lately?