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... [javascript] either loads the Flash page or the plain HTML page
My guess: If the HTML page is loaded by javascript then spiders will not read it as they will not execute the javascript.
A better implementation might be to always show the HTML version but to use javascript to hide it and show the flash version if flash is enabled.
What I did yesterday is to add plain HTML links to the two pages, but actually I can get rid of the starting page altogether if I make the starting page equivalent to the non-flash page. Which is basically what Vince said (and which I only read after haven written it myself).