Rated 4 out of 5 stars

Seems the author didn't update the addon to support sub directory for a long time now.

There are 2 new addons that can be tried:
1. https://addons.mozilla.org/en-US/thunderbird/addon/autoarchivereloaded/
2. https://addons.mozilla.org/en-US/thunderbird/addon/awesome-auto-archive/