There are the 7 velocity curves, have you tried them all to see if it makes a difference?
Even with a midi velocity of 1 from an external controller I get notes to sound, at least with short attack times. It could be a combination of velocity curve selection and patch envelope setup.
I've had some vintage gear do what you're saying as I play very softly and lightly, but I've never had that issue with the Prophet 6. Are you running the latest OS? As a last resort you might try clearing the calibration table, although I don't know if there are any related parameter variables in there that would effect velocity. Food for thought anyway.