junk mail controls
The junk controls are completely non intuitive and seem to not work at all when you get the pop up "Thunderbird thinks this is junk" I may not have that exact. Anyway there in NO option to say yes it is junk. The only option is to mark it is not junk. I don't understand why the most simplest things do not work yet there is all this arcane discussion about the most arcane things but nothing works. When this pop does not show up I can choose the junk button, So don't even go there....
Wšykne wótegrona (3)
When you see that popup, it means Thunderbird has already treated that message as junk, and it's not asking for your confirmation of the same. If the message is indeed junk, then no further action is required, meaning Thunderbird has done exactly what it was supposed to do. If the message is not junk, then you tell Thunderbird is it not junk by marking it as such.
Junk processing can be unintuitive in places. https://support.mozilla.org/en-US/kb/thunderbird-and-junk-spam-messages might help.
Stans is correct, I was about to post the same info.
However, on another note, are you aware that specified address books can be selected as whitelists, so email addresses/contacts therein should not get marked as junk? Also, if the email, regardless of being in a whitelisted address book, could get marked as spam by server filters before downloaded and therefore marked as Junk by Thunderbird if the checkbox to trust the server spam settings is selected.
Further, training what is junk is one half of the process, it is also necessary to train what is not junk if email is sent to junk and server spam filters are not part of the issue.
For anyone reading this info. The image below is the Account Settings > Junk Setting window which contains all the settings.