Oh, I KNOW how weird this is. That summary is correct. There isn't even a reason in the "Extra Options" plugin master file list, as it only requires "Core" to precede it. And so far only this one file seems to cause the change between the "selection" window and the "loaded" list (now that I understand how xEdit sorts). Somehow, at some point it is ignoring the date/time stamps of the selection sort before it loads the "masters" in favor of the order in the plugin in question even though that is not supposed to factor in.
But ... if I reset EO's date/time stamp to place it immediately after Core as it seems to want, everything seems to work as expected. I've adjusted the sort position of the remaining PN files "masters" and resolved my initial problem. It's just that something in the EO file that shouldn't logically be affecting xEdit's load order, is. Which is why I wanted to bring it to your attention. Whatever that something is, it might apply to some other plugin.
At this point I can understand if you want to just make a note of it in the bug tracker and wait to see if anything further comes to shed light on the matter. It's such a limited circumstance it doesn't warrant too much time in the scope of other more pressing priorities. It just the sort of thing that "bugs me", even though I know I have to let it go.