I am having the same problem with CCleaner 3.05; in my case, the following "unused file extensions" were reported after scanning the Registry:
.xpi (used by Firefox 4.0 for extensions)
.regtrans-ms (used by Windows 7 for staging Registry changes)
Note that last one (Win7 system file extension), which is for the Registry itself!
I am also having a problem that is preventing me from Restoring a CCleaner registry backup: Right-clicking on the cc-blahblsh.reg file does NOT display a "Merge" menu item, and double-clicking on the file just opens it in Notepad. First time I've had the need to restore a registry backup created by CCleaner, and I can't get it to work. I'm running Win7 Ultimate w/SP1.
