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It's a good idea to use semantic HTML and get things in the correct order so that all agents (browsers, bots, etc) can easily interpret the page.
I'm assuming you're using positioned divs and playing with the order of the divs in the code. Keep playing, it's usually possible to get a good logical order.
I looked at w3 and they said that it doesnt matter what the order is, but figured I'd check with what google is doing first though.
The six heading elements, H1 through H6, denote section headings. Although the order and occurrence of headings is not constrained by the HTML DTD, documents should not skip levels (for example, from H1 to H3), as converting such documents to other representations is often problematic.
Doesnt appear the w3 cares, but google might?