Smart Mailboxes Not Working Properly

To elaborate, I have 3 mail accounts, and 3 corresponding inboxes. I have also created some regular mailbox folders in one of the accounts. These regular mailbox folders are to hold emails that I have already dealt with and have names like "Misc" or "Family" or "Money" or "Work". These folders are all associated with one mail account. I move emails from my inboxes to one of these folders once I have dealt with the email.

Then the smart mailboxes look solely in my inbox for messages from specific people or with certain other properties like flags. One is specifically to look for inbox items from work colleagues. Another is for inbox items that have a red flag. Another is for inbox items that are from myself. Etc.

So when I am looking at a smart mailbox, I am looking at a subset of my inboxes. I should be able to click and drag an email message while viewing that smart mailbox and deposit that email message to one of those regular folders I created.

Again, it appears to work for a minute, but then the message pops back into the inbox and the corresponding smart mailbox. I would not expect it to work like that. This only happens if the message that I am moving is in a different mail account that the regular mailbox that I am moving it to. So if an inbox item is in Account 1, but I move it from a smart mailbox to a regular mailbox in Account 2, then the message comes back. But if I were to move that Account 1's inbox item to a regular mailbox in Account 1, then the message moves and doesn't come back.