On startup xfdesktop uses the 'custom font size' setting even if 'Use system font size' is checked. It gets applied if you uncheck and check the 'custom font size option' Reproducible: Always Steps to Reproduce: 1. 2. 3.
Interesting. It's actually not using either size. It's using the *default* 12-point custom size. So if you set the custom size to 16, then check the "use system" box, and restart xfdesktop, it'll use 12-point. I'm confused.
Ok, fixed.