Ok cool, I wasn't sure if you were planning to continue with it to start editing. I've done that sometimes. (Also I saw your mod was released! I hope to have a chance to try that sometime soon.)
Sorry if my post came off as overly sarcastic or anything. This issue has caused a lot of frustration for me personally, but I didn't mean to direct that towards anyone in particular. ModId seems to be the only program that is reliably stable and doesn't have certain extra complications like the black/white masks, but nobody seems to know what it does (and I didn't either, so I want to share this to help anyone else that runs into these problems).
The thing is, KeenGraph's problem happens during exporting. The right half of the sprite images are almost always supposed to have a red box in the gray area to define the sprite's collision area. In this screenshot of a row of images extracted by KeenGraph, you'll notice that half the sprites are missing that red box.
This issue only breaks the game once the blank hitboxes are imported, but if you want to use this to learn how sprites work, it's not going to be totally accurate to how it's supposed to be. Just something to keep in mind.
Also KeenGraph is sometimes unable to export mods that were edited with ModKeen, as I was just reminded while trying to double-check this.
You can do whatever you want of course, but I can't say I recommend KeenGraph for thoroughly studying other mods, unless the mod itself was already made using KeenGraph.