I think, but I'm not absolutely sure, that you're describing the default behavior of Thunderbird. The Junk button toggles between "Junk" and "Not Junk" depending upon the junk status of a message. You can mark something as not junk by marking it as junk twice. The junk button and clicking on the entry in the junk status column basically just toggle the junk setting. If you select a message and click Junk, and the button changes, then if you click on and open another message, the button should toggle back to Junk. If you use the keyboard shortcuts, you'll save yourself some confusion. Select a message and type j, and it will be marked as junk. Select a message in your Inbox and type Shift+j (=cap J), and it will be marked Not Junk, and the filter learns from that action. Select a message in the Junk/Spam folder and type Shift+j (cap J), and the message will be marked Not Junk and moved back into the Inbox. It's a muddle as far as I'm concerned, but it is what it is.