This page does not provide any information as to why Microsoft is now classifying CCleaner as a PUP/PUA, but Microsoft has stated that they do not support Registry cleaners and that they should not be used. In a new threat entry added today to the Microsoft Security Intelligence site, Microsoft is now classifying CCleaner as a PUA:Win32/CCleaner threat.
This ban was due to Microsoft's general stance that Registry cleaners and system optimizers can do more harm than good on Windows systems.