I've had more of a play, and it seems that it is an issue with one of my M5Stick devices, the YUN works fine with others. I'd still like to know what is wrong though, the device that is not working is brand new.

My Hat-Yun seems to be misbehaving. When powered by the M5stickC it works fine for a while running the sample code, and then the leds start displaying the wrong colours. If I power the YUN from the 5v input on the YUN it just doesn't work properly at all, with the leds being the wrong colours from the start. Any ideas folks?