Yep, I'm having this same issue. Tried deleting all remnants of Flash on my iMac, restarted, downloaded newest version again and still no luck. It's like Safari thinks the newest version of Flash is not compatible, despite recommending its download.
UPDATE: I resolved the issue by doing the following.
1. Make sure to install the most updated version of Flash. http://www.adobe.com/support/flash/downloads.html
2. Delete all references to Flash or Shockwave in Macintosh HD > Library > Internet Plugins > Disabled Plugins
Check to see if the version is older by looking at the Date Created sort field. If they are Flash related and weren't installed today, delete them.