after custom clean, browser cache, cookies and internet history are "skipped" even after I have stopped browsing. I physically have to go into my browser and close it. Never used to have to do that before.
It's been like that from the beginning. Browsers lock files that ccleaner needs to access or outright delete. The only way to unlock these files is to exit the browser completely. The last browser not to require closure was internet explorer (probably) 8.
When you first install CCleaner Custom Clean will show you this message if it needs to close a browser to clean it:
If you tick the box for "Do no not show me this message again" then it does exactly what it says and CCleaner will never show you that message again, instead if the browser is open then it will just 'Skip' the cleaning of that browser without asking you.
As Nergal says it's always been like that.
PS. Once you have ticked that box you can't undo it.
If you want to make CCleaner start showing that message again:
Uninstall/reinstall CCleaner.
Or delete the 'ccleaner.ini' which will lose all of your customised/saved settings.
(or you could manually edit the 'CCleaner.ini' file if you are an advanced user).