As you've found out powerful registry cleaners like Registry Mechanic, RegSeeker, etc., scan more areas in the registry thus they'll find more. However while they find more they can also easily tag valid stuff for removal which of course may not always necessarily be safe to remove and can cause problems ranging from minor to major. Major being the re-installation of applications that become broken after cleaning.
CCleaner's registry cleaner "Issues" plays it on the safe side which is a logical approach when dealing with the Windows registry. CCleaner happens to have one of the safest registry cleaning utilities, which in reality isn't as underpowered as many people may think, and it is capable of finding stuff that some commercial registry cleaning programs never find.