The folder name makes me suspicious.
Is Thunderbird putting them into the Spam folder locally, or is the Spam folder at your ISP? If, for example, you're using Gmail, then Gmail will create a spam folder of its own and put what it thinks is junk into it. Your TBird client then subscribes to that folder like any other, and won't know what's in it until you either click in it or otherwise do something to force a refresh.
Moving emails from there into your inbox may or may not teach the ISP's mail server what you're interested in. (And adding people to your TBird address list where the ISP can't see them won't have much effect either.)
Does any of that sound plausible?