One more update: I saw something I hadn't before when choosing a font to use for a new Panel:
I've never see this popup define fonts as "Embedded" or not. If that's always been that way, I've never seen the two at the same time (meaning I probably overlooked it before when it was all "Embedded" or all displaying the font path).
Regardless, if it's using "Embedded" to define what fonts are in the game atlas, that's incorrect, because the "playtime_512" is the 2048^2 size font you can see in the atlas screenshot I provided.
Additionally, for the fonts that display their filepath, there is no such path in my project that begins with "cgui/..." Even if it's truncated from something else, there is no such path.
Let me know if there's some meta-data somewhere that stores asset filepaths for NGUI. Hopefully that helps debug the issue or give you guys some ideas for me to try. I'm trying to move forward in the areas of my project until the original bug is figured out, but NGUI is pretty determined to screw me up it seems.
Thank you as always.