CCleaner is installed on a x64 system in the regular program path. Both 32 and 64 bit .exe are present and have not been renamed.
I am running CCEnhancer 3.3 from a backup directory on an external hdd, and it deletes the winapp2.ini file within that same directory. CCleaners installation file is in the same folder, although renamed.
Seems like a problem with version 3.3.