I use Windows 10 as my OS and Mozilla/Firefoxe as my web browser. I prefer not to delete Internet History as I find it a quick way to access regularly used websites and I have disabled all automatic browser cleaning. However every time CCLeaner runs, I loose all my browser history.
Are you using Health Check?
If you use Custom Clean instead then you can untick 'Internet History' for Firefox and CCleaner will then leave it alone.
The ticks/unticks that you can set in Custom Clean are only used by Custom Clean, Health Check ignores them and always does it own thing.
To change which method CCleaner uses as the default go to Otions>Settings and change the 'CCleaner Home Screen'.