I went back and installed 56 and tested.
I confirmed that it worked fine without dropping channels, but only tested on the one prop.
Then I installed 2017-4 and confirmed that the problem is still there.
If it makes a difference I'm using a pixlite 16 and the configuration is set up for a full 170 pixels per output. Problem doesn't exist in the preview screen only on the physical model.
I've gone into my setup and added three channels to all my outputs where I could and it eliminated the problem, but I should be able to set them for the actual number of pixels that I have.
I also just tested changing the maximum number of pixels in the controller to match and it made no difference.