I had the issue with ThunderBird 2.0 that I could not manually mark email as junk and have them automatically moved to the junk folder. I couldn’t even find the option. That’s because the option was turned off.

To turn it on do this:

Tools->Options->Advanced->Config Editor

Filter on “Manual”

Set mail.spam.manualMark to true.

Once I did this the “junk” sub tab option came up under the privacy tab (odd place to put it).

After this I could manually mark messages junk and off they went to the junk folder.

Thanks to Adam Weston on the #thunderbird IRC (irc.mozilla.org)

-CF