Alright, we've solved the problem, and have a good guess at why it happened.
Our PLC, even when we changed our WV project, was writing a TRUE value to $IN. This input is marked as used by the system, and (presumably) controls the activation switch. We didn't notice because we were doing grouping in WorkVisual, 16 bytes at a time.
1. Unlink any $IN bits marked with "SYS" in your PLC system
2. Upload WV project without IO linking (we factory reset the robot, but I reckon it doesn't matter so long as the IO
3. Cold Boot the robot.
Not fully sure that this is how to fix it, but we're pretty loathe to start trying to reproduce the error. To whomever reads this next, godspeed.