I just got CCleaner 1.27 to do a clean (I did all temp files) and then registry enteries. I made sure that the "MRU" option was ticked then I checked my registry. Some of the MRU's are not cleaned.
The point is here, CCleaner does not remove all invalid entries in the registry. Its not its main function but I do agree that it should be a bit better. Maybe 30 better in detecting and fixing issues. A few issues may not have significant results of slowing down your PC. I personally use 3 registry cleaners just to make a deeper clean.
I have noticed lately that CCleaner finds nothing to clean in the registry except unused file extensions. This is using version 2.27.1070 under Win 7 64 bit. I think it used to find more than that previously. All boxes checked in the cleaner tab. I have removed and installed from a new down load and find the same. The PC in question is used to test various software so many programs are installed and later uninstalled but CCleaner finds no leftover keys. Any ideas short of a OS reload to prove whats wrong?
@wonderwrench - maybe you've already fixed the majority of discrepancies, and the new software you've been un/installing is tidying up after itself properly.
You say ".... prove what's wrong ..." but there may well be nothing wrong! It's certainly not worth an OS reinstall.