There have been many viruses that remove the contents of the start menu. They move them to %TEMP%\SMTMP, SMTMP1 and SMTMP*. CCleaner is a great program to clear out garbage that slows down scanning but it will permanently remove the entire start menu on infected machines.
Please implement an exception to file removal for folders named "smtmp" and its derivitives (smtmp1, smtmp2, an so on). Here is a good example of a recent version in a string of infections that damage the system in this manner: http://www.bleepingcomputer.com/virus-removal/remove-system-check.
I thought about this somewhat, & my conclusion is that under normal non-virus infected systems, CCleaner is pretty safe to use & this does not happen.
CCleaner is meant to be a system cleanup utility & not an anti-malware or anti-virus solution. The efforts required for this would be astronomical. This may sound like a good idea on first thought, but consider the following:
If CCleaner were to implement this, it would also have to do the same for all other malware infections, & resultant in a CCleaner that would gradually denigrade in performance & trash removal capabilities as thousands of new antivirus & antimalware pattern sets to scan for before removing trash were set into place.
CCleaner would thus become bloated, slow, & nearly as useless as the trash it is designed to remove.
* I would hazard the guess that this would be the users responsibility to check for & properly remove malware & viruses, & not Piriform.