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When I login in Yahoo Mail, I am logged out automatically from Messenger (the real one).
That's because I appear in Yahoo Mail Chat list.
How to stop that, that is how to stop being logged out from Messenger?
You need to sign out from the messenger in Yahoo Mail. Click the yellowish lightning icon next to Online Contacts (it's grey in the screenshot because I'm signed out).
Options -> Messenger options
Always sign out here
Yes, permanently sign out and close the web site.
Required, but never shown