Hi, I was having this issue as well. While this explains it, I am still not sure what I can do.
I created small black and white squares for a lot of GUI filler, such as simple progress bars. I chose 9px by 9px because I figured the edges would be blurred and I would be able to crop in on the atlas. It worked fine until I updated the atlas and my nice clean edges went blurry because the image was reduced to the crop dimensions.
1) Is this the expected atlas behaviour?
2) Do you have any tips on how to make this work?
Cheers,
- Rafe