CCleaner deletes Topsites.plist in C:\Users\user\AppData\Roaming\Apple Computer\Safari when the internet history for safari is specified, but Topsites.plist is for so-called speeddial for safari, and it should not be cleared.
Please consider this problem.
P.S.
Is there any documents or help file that explains what actual files and directories are deleted when cleaning?
top sites is meant to be cleaned. exclude it in the exclusions option if you don't want it removed
run "c:\program files\ccleaner\ccleaner.exe" / export
with the quotation marks replace c:\program files\ccleaner with the location of your ccleaner. it will export all the inbuilt cleaning rules into plain text ini files.
not so sure that ccleaner can see a visible difference between the two. I don't use safari except to test pages on multiple browsers so I've never used top sites