So after a fun filled day, I figured out something that must be obvious to everyone.
Unplug your MIDI Out cable before flashing your chip when monitoring in MIDI-OX. Sure, leaving the cable in will yield a quite pretty rainbow pattern on strange midi commands like the purple "PC: Marimba", but every once in a while (often enough to take a major part of your day), the thing will default to a dreaded yellow Song Pattern signal. Your potentiometer information will be trashed and stuck in this crappy color!
You'll be sitting there wondering "what the heck?" It was just working!
Friends don't let friends flash chips with anything plugged in.
Is this common knowledge to everyone else?