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I'm certainly not a javascript expert either, but if ibooks is running said script before you flip to that page I would think it is because the "page" is run when the file (chapter) is opened. If you can't get Doitsu's method to work, perhaps putting that page of text and associated JS into its own file will do the trick?? It may look funny when the epub is reflowed - the previous page could cut off midway down the screen - but at least you know that JS won't run until that page is opened.
FWIW
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