It's cold comfort, I know, but I am having exactly the same problem with CCleaner on two Win98SE boxes.
Versions up to 2.14 have worked fine for years. Then I updated to the latest v2.16, and the "Clean" part of the program stopped finding anything to remove. Unfortunately I did not keep the v2.14 installer, but I have still got v2.07. I am now using this, and the program works again. So something has changed going from v2.14 to v2.16, making the new version incompatible with my Win98SE installations.