After I updated the PGE editor and the SMBX-Int config pack, there started to be black and white pixels filling the part of a BGO that was not replaced by an image. This is probably really confusing to read, so here is a picture:
This image is a PNG, and it is smaller than the original by 2 pixels in width and height. You can see that there are random pixels in that space that are usually black and white, but there are occasionally other colors (like that bit of brown on the bottom). This was not an issue before I updated. These weird pixels are not consistently visible, but they show up in most tests in SMBX. I don't know how PGE could have caused this (LunaTester maybe), but there wasn't anything else I did that could have messed this up.