Just for anyone else having trouble with minifying, errors in your code can affect it. I think that's what was messing me up, I had a couple of things that weren't causing error messages or being picked up by JSHint but they were stopping minification.
Espruino is a JavaScript interpreter for low-power Microcontrollers. This site is both a support community for Espruino and a place to share what you are working on.
Just for anyone else having trouble with minifying, errors in your code can affect it. I think that's what was messing me up, I had a couple of things that weren't causing error messages or being picked up by JSHint but they were stopping minification.