It does sound like under watering. New bark does not retain moisture very well. And these don't want to dry out. I have also bee told that heat stress can cause the spots. I struggle growing these and get spots on them no matter what I do.
Welcome. In my experience (limited, I admit ) Zygos and Oncids both are very difficult to grow with out "crud" (spots on the leaves ). I have been told by pro growers that it can be too much humidity, too much light, too much heat. I don't know if anyone really knows what causes them, but they don't seem to interfere with growth or blooms.