Maybe try installing it by downloading it from apple.com/safari/download instead of software update, sounds like SU isn't updating your "receipts" properly.
...For whatever reason Tiger/Leopard users of Safari on a PPC e.g. G4, are seeing this prompt. The fix is on Apple's end. To remove it from Software Update, open SU, and select "check now". Once the check is complete, highlight Safari. Then, in the Update Menu select "ignore update".
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Wouldn't doing what you suggest prevent me from getting valid update notices in the future?
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No, when ever used, the "ignore" option applies to only that particular item/version. If necessary, the action can be reversed via Software Update.