CCleaner was configured for a while to clean Opera 10 Beta, but since the official release of Opera 10 Final, it's understandably been configured to clean the default locations of the Final release.
I had the same problem as you, as I installed all versions from the first Opera 10 beta to the final release in the same folder. Unfortunately, the install of Opera 10 Final left the installation folders with the Beta name. I personally blame Opera for this, not CCleaner.
My only solution was to backup necessary settings files and folders, completely remove all traces of the Beta install, and then do a clean install of Opera 10 Final.
It has been discussed before, and maybe this will help. It refers initially to Opera 9 folders, but the problem is the same.
http://forum.piriform.com/index.php?showtopic=24035If there's an easier way to do it, I'm not aware of it I'm afraid.