Working backwards from Alien Power Matrix

Update from the maintainer

Confirmed, and your own follow-up was the clue that cracked it, so thank you for that. It is not a missing recipe. Three of the Quantum Encoder recipes in that chain give off Dark Matter Residue, only Dark Matter Crystal consumes it, and the ratios do not line up, so the balance ends up holding residue it cannot put anywhere. That forces the whole loop to solve to zero, and the planner then clears away the belts that are carrying nothing, which is the broken wiring you saw. With every alternate switched on it picks the residue-only Dark Matter recipes instead and the surplus lands at exactly zero, which is why it works for you that way. Marking this in progress. The fix is for the balance to put a sink on a byproduct that nothing can use, rather than quietly wiring it to a consumer that cannot take it all.