My bad on the version, its still 1.44.
It's quite odd that it works when you run it manually, as CLI will boot up the GUI apply the settings and start, then quickly hide the GUI before you can even see it.
I will boot up again and get this working in rimmington
Edit: ok so this is the stupidest bug ever and I will work to fix it, i dont know how long this shit has been a problem for.
Long story short its because when loading the config, it doesn't set the 'Ores' drop down box to Iron, and even though you selected the rocks manually, it hasn't figured it out so its busy trying to mine tin in the same spot as iron (which doesn't exist).
I've pushed out a fix (actually version 1.45 this time) to make it force the drop down box to the right option even though its disabled, it may take 24 hours.
Note: its not just CLI, its all config loading in general so chances are a lot of people were affected by this shit