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I have little/no experience with PWM, but are you sure about that much capacitance across the diode? At a higher modulation rate the cap will absorb the pulses and you'll just get a wiggling output rather than a pulsing output.
Depends on how fast you pulse it and how much current you are driving. I would suggest using a scope to find a good value where you don't have a lot of overshoot but still good capacitance.