I usually install only Microsoft software and few non-Microsoft system utility packages under the classical C:\Programs\... location. All other software goes to D:\, while other drives are for project or user data.
If data to be cleaned is located in run-time directories of software, CCleaner will only find it if it's the %programfiles% standard location, although the installation entry in the registry clearly says where the software is installed. It my be useful to introduce another %...% variable in CCleaner winapp/winapp2.ini files to refer to the respective entry's installation directory. For the time being, my solution is to add a separate entry for some software packages, that point to the respective D:\ directories. It could be done easier...
Cheers,
--panoramacat.