UserFriendly - 2:18 am on Jul 11, 2010 (gmt 0)
I think it's probably the moving of the navigation links to the "left" (I assume you mean that the actual markup for the links now comes before the main text, whereas before it was after the main text.)
Have you tried moving the navigation box back to a position after the main text? You can use CSS to position it wherever you like the look of it, but remember to take a look at your pages in "user styles mode" so that you can see how your page reads to users without graphics and CSS enabled (usually people with sight impairment). Perhaps offer a link down to the nav links for such users, and then use CSS to hide that link for CSS-enabled visitors.
And is your main text nicely broken up with suitable h2 and h3 headings? (I'm pretty sure Google gives keywords in these headings greater weight.)