We've spent a tonne of time investigating this. We tried to reproduce it internally and weren't able to. We scoured the code and found no issues. Earlier this week I asked people who were experiencing this to send me their accounts so that we could look at their specific cases to see if something unusual was happening. In two of those cases, the players messaged me afterwards to say that they'd found those masters since. In all of those cases, we tested dozens of maps on their accounts and found that all masters had spawned.
Right now one of our sys-admins is working on a script to scan the instance logs of these accounts so that we can see exactly how many masters have spawned for them and which ones. This is taking a while so it's unlikely we'll see results until early Monday.
The rate that masters appear naturally in maps is 10% and therefore 2% per master. Maps are also limited to one master at a time. This means that if you're forcing masters to spawn through the use of Atlas missions, Sextants or Prophecies, a master will not be able to spawn naturally for that given map. (Cassia and Tane are not masters.) This means that if you're not forcing masters to spawn at all and you run say 50 maps, you might only see each master once or perhaps more or less based on your luck.
It's possible that they are simply rarer than people expect but I'm hoping the results from the logs on Monday can help shine more light on the situation because it's definitely a concern that so many people are reporting this. I'll follow up on Monday and let you know the results as soon as I can.