I see, I’ll keep that in mind.

But even if the problem is in adjusting color palette, why simple repositioning of the transparent color fixes the problem completely? I don’t change the color itself, I don’t change colors of other pixels, I just move one color in the index table, and that’s all.

PS: Since I found how to eliminate the problem on the plugin’s side, it no longer bothers me as itself, but I’m concerned about possible bug in EmEditor which caused such strange behaviour.