The issue was using a slow task class for the AsFltGen library. Since the task class must be run to update/send the next set of flat stream iomapping, in a slow task class the process took long enough to visibly desync the stack lights.
Moving the task class from a 100ms to a 3.2ms (PLK/X2X at 1.6ms) removed enough delay that the lights should appear to the human eye as in-sequence.