Found it! Was pretty interesting; there is indeed an "environment variable" not being set:
The bug is in both Stella and the Harmony firmware for emulating the SuperCharger which made it tough to find; I check my builds regularly in the emulator and semi-regularly on real hardware but I had been taking a shortcut and using the Harmony in the Parlour with the Vader as real hardware instead of the Junior in the basement with the SuperCharger.
Turns out I was playing Clu and had to use Tron to find the bug (Tron is a trace program that you write). Does anyone else ever code with Tron instead of using the debugger in Stella?
This is an example where you have to use Tron because you can't use the debugger - there's no 6502 Assembly code to debug in Stella when the bug is in Stella!
The game I am working on is running inside the ASDK Framework like DodgeIt PA in my signature, only it's using the SuperCharger version.
As a fun programming discussion/exercise, would anyone else like to try finding this bug with Tron or any other method (I'd be curious to see)? I can provide the commented asm for anyone who is interested.
I will share details on the bug presently so Stella and the Harmony firmware can be patched for better compability with the Starpath SuperCharger and the ASDK SuperCharger Gold Edition
Also curious if the Kroc and the Cuttle have this bug if someone could try the binary on them; you should see the sprites vibrating like they are stuck in molasses instead of moving all over the screen if they emulate the SuperCharger correctly.