I don't know if this is possible to be fixed by MyM, but there is an issue that whenever blocks are placed any distance above a breeding area, the pokemon are not visible and are therefore making players unable to check how much time it will be before an egg is laid. This is very inconvenient because chunk loaders do not exist in 1.10 as of now and if you want a 1 chunk breeding area, the pokemon disappear. Please fix this issue if possible.
I had the same issue when I tried to make a underground breeding chamber. From what I could find while researching it, the breeding area requires a clear line to the sky to function properly, so it is most likely a mod limitation.
Hello MVP, I'm looking into your issue and I have a quick question: How far above the breeder is your roof? I only ask because I was able to place a dirt roof over one of my ranch plots 5 blocks above my floor and my Dratini's are breeding just fine, I'm able to see their progress hearts and all. Keep in mind the rancher will try to calculate off of the highest block, up to 3 blocks above the rancher. Your roof may have been too low, and it may have tried counting your roof towards the happiness of your Pokemon and determined the environment was unsuitable for what you were breeding at the time.
It does not affect the breeding process, but if the roof completely covers the breeder the pokemon will disappear, I have tested this with as much as 10 blocks above the breeder.
That's a little strange, I had a roof over one of my plots for 24 hours and didn't notice the breeding pokemon vanish.
Since we haven't heard anything back about if this problem still persists I'm going to mark this thread as done.