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/mode reports controller=running at the spawn, so the reference dump raced grblHAL's init writes and captured the supervisor's motion-probe values (motor_lock 0, step_freq 10000, y_mode at the module default) instead of the resting state. boot_reference() now waits for the controller's markers (step_freq/motor_lock/y_mode at their fixed values, bounded 20 s, GRBL mode only) plus a 1 s settle before dumping, retakes a saved reference that shows the pre-config state while the boot is still fresh, and marks it otherwise. Tests cover the wait, its timeout, the non-GRBL no-op, the pre-config recognition and the retake.