So... did you enable both accounts for POP3 access (I think Yahoo! only allows POP3 access for pay accounts, but I could be mistaken)? Have you double-checked all settings for those accounts? Have you tried deleting both accounts (back up the e-mail if you want it before doing so) then re-adding them?
You're going to have to be our eyes and ears on this -- simply saying one account doesn't work and the other one does isn't enough information for us to try and troubleshoot the problem. Be as verbose and specific as you can so we can help you. Are you using the exact same SMTP and POP3 servers for both accounts, with the correct login information for each?