Junk mail confusion - is this spam?

I have long been confused by certain behaviour of Mac Mail.
When Mail identifies spam (on my Mac, at least), it marks it by changing the text colour in the preview pane brown and moves it to the Junk folder, as per my preferences.
However, I get some mail which does not qualify as Junk Mail or Spam as, according to the rules, it is from a previous recipient but Mail leaves it in the Inbox (or moves it, depending on my custom rules) and marks it by making the background of the preview pane brown but the text is still black.
If I click on this mail and mark it as spam, it then moves to the Junk folder. If I then click on it and mark it as not spam, it changes to the normal black text on white background in the preview pane - so there is something which makes me think that this is related to Junk/Spam. I have messed around with flags but they do not seem to have anything to do with this.
I really don't have a clue why this happens and have searched for years to find out without any success.
Any ideas?

In addition to Corky's suggestion on the right hand side of your profile page is this box:
Click  Manage email notifications.  This manages any current email notifications you are receiving.

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