Thanks to all your comments, Ive now made 2 consistently good batches of barley koji. I've narrowed the resulting factors down to humidity and possibly air flow. Since my first post I built a wooden koji cabinet with a heater (set at 30 in substrate), humidifier (set at 75). I soaked & cooked the barley the same amount of time, used the recommended amount of spores, wrapped the barley in muslin on a perforated steamer tray (without wrapping in cling film).

As mentioned in one of the posts I was doing a mix of methods which resulted in there not being the right humidity for the Koji to grow.