I've had this problem as well, mostly with DeRLE.
I was playing around with the standard cursor (which now switches from easter colors, to the standard red with green fillings in the moving arrows to the standard red and back again ) and I began trying to edit some of the weapons to create oddities that would make the game a bit more eye pleasing (the superheavy blaster being a bit redder, etc). After finding a particularily easy to deal with RLE8 from Nova Graphics 2, I dropped it into DeRLE and searched and searched for the outputted PICTS to edit in Appleworks.
Finally, after doing this multiple times in many styles (separate folders, different locations), I came to the realization that DeRLE was creating invisible RESEdit files. Invisible ones that I can't delete now clutter my desktop and tons of folders. And worst off, they're not even correct! All I have are superheavy blaster masks with the color removed!!!
Try searching those folders with RESEdit's "open" window. If you find them, they'll probably be black and white holes in the black background, same as here (or not, since you were doing the opposite). If you do find them, if you can figure out a way to get rid of them, please tell me!
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When viewing a Terrapin for the first time, I realized that anything flies-if you throw it hard enough!