This happened to me, and there is an easy, if not incomplete solution. The problem is that none of the "password" recovery methods work, and Yahoo's "help" services are useless. After Yahoo started requiring personal information, like phone numbers, address, other e-mail accounts, etc, to gain access to your years worth of e-mails and Messenger chats, I found ways to bypass the security questions. The consequence is that the only way I have access to my Yahoo e-mail is to log into Messenger with the stored password, when the "you have mail" icon appears, I can click it, and it opens into my Yahoo email account. However, I cannot log directly into my Yahoo e-mail, because it says that my password is wrong, or expired. I don't quite understand how the "stored" Messenger password works, but I can't manually type it in and it doesn't work, but regardless, that's the situation.
So when I moved to a new computer and tried to set-up Yahoo, Messenger wouldn't accept the password. I KNOW the password, but the software doesn't accept it. Googling for ways to hack the software or the password was useless, and it appears that the current versions of Messenger are not "hackable." This is how I transferred my old stored password from my old computer and Yahoo Messenger to my new computer and updated Messenger.
1) Install Yahoo Messenger on the new computer. I was moving from Windows 7 to Windows 8, and had Yahoo v. 11 on the original and new computer.
2) Copy the old Yahoo files to the new computer--these were in ProgramFiles directory--my profile, old chats, etc.
3) The stored password is saved in the registry, so this has to be copied over.
a) On your original computer, open registry by clicking the start menu and "regedit"
b) Navigate to HKEY_CURRENT_USER\Software\Yahoo\pager -- right click, "export" and save it someplace handy.
c) Copy this file to your new computer and double-click.
That's it--it should automatically install. That's what worked for me. Now the username and password automatically populates the Yahoo Messenger fields again, and I can again access my Yahoo e-mail when the e-mail icon appears. It doesn't seem that you can extract the original password from the registry key (ETS), but copying the entire key to the new computer is sufficient to make Yahoo Messenger work again.