Sorry, that you should encounter this known issue. At least, if I understand you correctly, it seems like the same problem as these people have:
The same here: https://animationpaper.com/forums/topic/glitched-brush-textures-glitched-squares-when-using-ctrl-z/
I can tell you, that we are aware of it and we are working on a solution. We hope to have it solved with our next release (Alpha 4).
I’m really sorry that I recommended Animation Paper as being much better than PAP – and then you run into this. Bad luck. It works very well for the vast majority. And it will work well for you too – when we find a solution…
Thanks,
Niels