The SHTML pages and SSI should not matter. You'd need to spider your site from a page with links to other pages. Starting from the main Flash page, without links elsewhere, won't index the site, as PhpDig follows links. Enter a link from an inner page in the textbox, click the 'no' radio button, set 'Search depth' to a large value, set 'Links per' to zero, and give that a shot. Also, as an aside, the home.shtml page seems to be missing an end DIV tag somewhere.
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