Hey -- that might be why I'm not having that problem so much any more. I recently deleted all cookies from my drive and changed my IE security settings to refuse all cookies except from websites that I tell it to accept, and I'm only doing that with a few sites (mostly forums, a few stores). IMHO there is no legitimate reason for most websites to use cookies, and in fact when I was accepting but watching them I noticed the great majority are from popup and banner ads (which IE considers a separate website, usually). There are a variety of ways advertisers abuse cookies to invade your privacy and target you with web ads and mailspam.
It never occurred to me that accepting cookies from one website could screw up the cookies of another website, but maybe so ... and if so, that's yet another reason not to allow websites that don't have any legitimate purpose for cookies to put them on your system.