This seems to be a problem in the latest update to the extension, judging from the reviews.

https://addons.mozilla.org/thunderbird/addon/theme-font-size-changer/reviews/

If you want to try rolling back to an earlier release of the extension, you can check the following page using whatever methods you can in Thunderbird (there's a link to this at the bottom of the main page, in the Versions section, if needed):

https://addons.mozilla.org/thunderbird/addon/theme-font-size-changer/versions/

While it didn't fix the latest version, it got me back to an older version that does work. Thanks!!

Joemac8 said

When my Mac updated to Thunderbird 45.3.0 from 45.2.0, my font went from great to really small. I have removed and reinstalled Theme & Font Size Changer several times but no luck The tools menu from Thunderbird Menu bar has no option showing Theme & Font Size Changer. My font is so small I have to use a magnifying glass to read e-mail. Everything with Firefox works fine. I downloaded Zoom button but had the same result. I reloaded Thunderbird 45.2.0 and installed it but no joy.