I upgraded to Yosemite OSX 10.10.1 and most of the the favicons disappeared in favorites folders.

I upgraded to Yosemite OSX 10.10.1 and most of the the favicons disappeared in favorites folders. So much slower to find folders.

Returning to Mail Preferences - Junk Mail, in the section
When junk mail arrives:
select mark as junk mail but leave it in my inbox
This should then give you the opportunity to mark it as Not Junk
and after several days it may improve.
I say 'may improve', based on my experience of when I upgraded to 10.5 a few years ago.  It took a while to learn what I kept insisting was not junk. It is a slow learner but it got there.
P.S. When you are satisfied it is identifying junk reasonably accurately, you can change the Preferences setting back to  'Move it to the Junk mail box'
Message was edited by: roam

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  • Since upgrading to Yosemite, my outbox clogs up and doesn't send all emails.

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    Thank you for using Apple Support Communities.
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