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I don't have it set up so they can join and leave groups. Plus it's changing all of them at once, including people who haven't been online for at least a week.

Here's a list of my active plugins:

• Simple Audito Video Embeder (2.0)
  
• Automention (1.3.2)
  
• MyBB Chat by Chatwee (1.0)
  
• Custom Status (1.8)
  
• Disposable Email Blacklist (1.1)
  
• DVZ Mentions (0.6)
  
• Glitter Thread (1.0)
  
• Usergroup Legend (1.2)
  
• Many New Posts (2.0.2)
  
• Mood Manager (1.2)
  
• MyAlerts (2.0.2)
  
• MyProfile (1.2)
  
• MyCode: [spoiler] (1.2)
  
• NewPoints (2.0)
  
• Private Message Log (1.1)
  
• Portal ReadMore Button (1.2)
  
• Rate Me a Funny (2.0.8b)
  
• Redirect to thread (0.1)
  
• Related Threads (1.0.1)
  
• Social Sites (0.3.3)
  
• Table Generator (2.0)
  
• Tapatalk (4.5.5)
  
• UA Plugins - Messages (1)
  

And the group promotion is definitely 100% turned off?

Correct

Update: The problem seemed to be if I assigned the same rank to both primary and secondary it would cancel out I guess. I tried just giving them a primary rank and not an additional one and it seemed to stop putting their primary at Registered.