I noticed cookies from Yahoo and a few other websites remain despite manually deleting their cookies that appear in the OPTIONS>COOKIES menu. This seems to have just started happening. Using Win10.
You say "manually deleting"; is there any particular reason why you didn't use CCleaner to delete them?
(Or do you mean that you right-clicked and selected 'Delete Now'?)
Do you have your browser synced?
See this for why syncing, and other things, will bring cookies and files back after cleaning:
https://community.ccleaner.com/topic/52668-tracking-files/?tab=comments#comment-300043
Is the browser fully closed, ie. nothing still running in the background?
Try:
Open Chrome > click Menu > Settings
Click Advanced > System
Move the "Continue running background apps when Google Chrome is closed" switch to the left, to the "Off" position