I'm having the same problem. CCleaner only shows 3 cookies:
Cookie:larry swinney@yahoo.com/
Cookie:larry swinney@www.yahoo.com/
Cookie:larry swinney@tv.yahoo.com/
It doesn't list the other cookies I want to keep, so I can't move them into the protected area. These are the cookies not listed:
Cookie:larry swinney@foxnews.com
Cookie:larry swinney@google.com/
Cookie:larry swinney@military.com/
Cookie:larry swinney@nypost.com/
Cookie:larry swinney@sdc.tvguide.com/
Cookie:larry swinney@support.microsoft.com/
Cookie:larry swinney@tvguide.com/
Cookie:larry swinney@winxpcentral.com/
Cookie:larry swinney@www.military.com/
Cookie:larry swinney@www.slyck.com/
Cookie:larry swinney@mail.military.com/militarycom
Cookie:larry swinney@www.foxnews.com/video2/
I just noticed this recently, but it may have been going on for awhile. In earlier versions, it used to work fine. I have checked my "temporary internet files" folder and the cookies are there, but CCleaner doesn't list them.