I can't think of any reason off hand, but try this:
1.
Create a new scene to reset all data.
Select the tileMapEditorData object, switch to inspector debug mode, and then expand "Palette Brush".
Enter 0 into the Brush Hash field - this will reset the brush hash and force a rebuild next time it is used.
Open up your scene again, and see if it has improved?
2.
Open up the sprite collection, look for sprite id = 0, does it exist, and is it a decent size?