Is this by any chance a Free Yahoo! account. I think [this|http://answers.yahoo.com/question/index?qid=20071113165925AAUfNpF] is the issue now. This is what tipped me off to this.
This server may required an additional fee for Pop access
I misspoke (miswritten) in my previous post that I had a free account. This happened to be an old email setup that got transferred to Yahoo! sometime in the past. Yahoo! upgraded me to Yahoo! Mail Plus for free. (I do have a current free account, but it is only used as a push email account to my iPhone.)
I am completely out of ideas now. I don't know of anything else it could be. If your account is a Yahoo! Mail Plus account and these problems are occurring, I would contact Yahoo!. I really don't think there is a problem in Mail.app for OS X.