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Uninstall ClickToFlash and install ClickToFlash again from here (NOT clicktoflash.com):

http://hoyois.github.com/safariextensions/clicktoplugin/

Jonathan Rentzsch doesn't update his version of ClickToFlash (which is probably what you have) anymore so it doesn't work with Safari 5.1. Mark Hoyois does though and it works perfectly with Safari 5.1. The main difference between the two is that Rentzsch's one is a WebKit plugin (which are longer supported in Safari 5.1) and Hoyois's one is a Safari extension.
 
Strange, even the links posted do not make it work on the new safari for me, kind of disappointed missing out now
 
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