I'm afraid I have no experience growing Vanilla orchids, although I would like to try one day. That said, I am concerned that you say they are planted in "a good matrix of decaying matter and soil" when Vanilla orchids are epiphytes; they need excellent drainage.
The brown spotting could be either a bacterial/fungal problem, or damage due to cold/low humidity - it is hard for me to say as I have no experience growing this genus. You mention that there is a "lack of heat and humidity"; what temps and humidity are you seeing up there at the moment? Down in here in winter, I have to protect some Cym species and their hybrids because they are vulnerable to windburn (cool, dry air damages the foliage).
