Does your anti virus program have an anti spam or scam settings. They often make a very special job of messing these things up, and hide their involvement behind a single check box in the anti virus program talking about enabling an anti scam or spam toolbar or other related features.

I've tried 3 different antivirus systems so far. MS Defender. Avast. Sophos. Still can't move those emails back to inbox or filtered folders. Good news is that now more emails are going to the right folders but not all of them. My ISP is going nuts because all their emails are now going to spam as well. Movement forward.

Captain Quack.

I think I have noticed something when I was testing this issue with clawsmail. Somewhere in TB the emails that kept getting sent back to spam had been tagged spam and there was no way to remove it. Junk yes. Spam no. That explains the reason addresses I have whitelisted on various servers have had no effect. Anyone have any idea where to go to look and see where TB might be doing this?

I have exactly the same problem and still can't solve it. I have been using Webroot antivirus for a few years now but the problem only started about 6 months ago. The only difference to your scenario is that I am still running windows 10

That's almost identical to mine. Nothing had changed and then one day it started happening. What really gets me is that I've done 5 or 6 uninstalls of TB using a 3rd party uninstaller to get all the left overs out and 2 or 3 full system wipes and full reinstall's. What is holding this settings between all that and where is it to edit out?

https://support.mozilla.org/en-US/kb/thunderbird-and-junk-spam-messages describes Thunderbird's spam settings. But it only applies to messages which have the junk/spam icon set.

Things other than Thunderbird can put messages in the spam folder and they will not have Thunderbird's junk icon set. Thunderbird has no control over how these messages get put in the spam folder.