Ok so what's happening is I will get emails from say, "Bob". All of Bob's emails show up on the "Updates" tab where I want them. Every so often a few will pop up on the "Inbox" tab. The problem isn't so much that they do, but its a pain to fix. Even though that particular email from Bob shows up on the "Inbox" tab, it still shows its labels as "Inbox, Updates" just like the ones that are showing up in "Updates" only.
Now, if you remove the label "Inbox" then the message vanishes to archive. If you move the email from "Inbox" to "updates" then the message vanishes to archive.
In order to get the email from Bob showing up in "Updates" again and in the order it arrived you have to remove the "inbox" label, leave the "updates" label. Then go into "All mail" to find it again and click "Move to inbox". This reapplies the "inbox" label along with the "updates" label so it looks just like it did originally but now it shows up in updates only and in the order it arrived.
I'm doing this all day long to keep certain emails in the Updates tab that sneak their way into the Inbox tab when they arrive..