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Sometimes you might need to use a timedelay on the spindle.0.on to ensure the air circuit gets up to pressure before the spindle actually spins.

I can't help but wonder if a pneumatic presssure switch would not be a better safety feature. They are not expensive. Tie it into estop or motion.inhibit somehow. 

Slow your velocities down and see.
I think the sign is the opposite of LATCH_VELOCITY

One of my machines:

MIN_LIMIT = -106
MAX_LIMIT = 0.01
HOME                    = 0
HOME_OFFSET                = 1
HOME_SEQUENCE            = 0
HOME_SEARCH_VEL            = 5
HOME_LATCH_VEL            = -2
HOME_IGNORE_LIMITS    = yes
HOME_USE_INDEX = NO

Are you using steppers or servos?
It's possible you are observing  low speed stepper harmonics. If that's the case, the solution would be to alter the motor gearing to avoid low motor speeds in the harmonics range.