******This might just be the answer*******
I didn't notice when I went back to Version 5.40.6411 but at the top of the list of 'Cookies to keep' there was a BLANK space which I clicked on and it highlighted the space.
I then moved to the 'Which side do you want it Arrow Head and moved it to the 'Cookies to delete' side of the page and blow me down with a feather about 300 Cookies suddenly appeared!
I then wiped out all of the 'Cookies to delete' by running CCleaner and those cookies were erased.
I then reinstalled Version 555, closed the program after installing and went and 'collected' a few new cookies that I didn't want after I had finished.
Then after closing Chrome I opened up CCleaner/Options and the 'Blank' space was no longer there, while the cookies that I didn't want to keep are all lined up on the left hand side of the page to be removed!!!
Yippee!
I hope this works for you as it seems that 'Blank Space' at the top of the 'Cookies to Keep' is also keeping the ones you want to get rid of!!
Good luck!