Had the same problem. It was somewhat 'solved' by setting the junk
filtering options that are under 'Account settings'. When I set these
too, instead of just the global settings, the junk messages were
correctly moved to the junk folder, behaviour as expected. I feel this
is more of a workaround than correct behaviour of Thunderbird, but
still.

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Thunderbird does not move junk messages into junk folder
https://bugs.launchpad.net/bugs/155759
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