Mail moving non-Spam message to Junk, and not marking them as Junk

I have seen a couple of other discussions related to this, but no relevant answer. I will try to phrase the question completely.
I am using OS X mail with no additional Spam filters. My email service is mac.com/me.com/iCloud (I am wondering what the next iteration will be).
I am on the latest version of Yosemite, and my Junk Preferences are:
So, two different, but related, problems:
Mail does a pretty good job of catching real Spam and moving it to the Junk mailbox. HOWEVER, it has various ways of marking said messages.
1) No Brown Color, No Junk Mail Flag
2) No Brown Color, Junk Mail Flag
3) Brown Color, Junk Mail Flag
On the issue of false positives, Mail also does a pretty good job, but it also makes mistakes 2 to 3 times a week (not a big deal, unless it is an important email). In these cases, the message IS moved to the Junk mailbox, however it is neither in a brown font color, nor is it flagged as Junk. In all cases, these messages (I checked) are either in my Contacts and are among my Previous Recipients or BOTH (sometimes I will have 3 messages in a day from the exact same e-mail sender, and 2 will be in Inbox, and 1 will be moved to Junk). Obviously I can not mark these as Not Junk, as they are not marked Junk!
To the best of my knowledge, I have NEVER marked messages from these senders as Junk.
I have just changed things over to Perform custom actions, where I have been very explicit about what is junk, and what to do with it. Hopefully this will fix things, problem is it will take a couple of weeks to be sure. So until then, I thought I would throw this question out there.
Thanks!

1) No Brown Color, No Junk Mail Flag
2) No Brown Color, Junk Mail Flag
Your e-mail provider may have marked these as junk since there is no color. Check the web site to see if you can make an adjustment there.

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