Very difficult to tell for sure, but from your description you have experience with raising other Masdevallias. Is it in shade or if indoors where there is 500-1500 foot candles (indirect low light where there is slight shadowing) and with temperatures no lower than 45 degrees F., but no higher than 75 degrees? Also water with steam iron water 2-3 times a week, allowing it to dry just slightly before watering again. Black spots can occur due to warm temperatures (although this time of year, it should not be a problem in your area) or a bacterial or fungal problem. You really need to show your orchid to one knowledgeable about Masdevallias or to the person you purchased it from to get confirmation about the reason for this problem.