Confusing Arduino Leonardo PWM
Pins 9,10,11 should be working off TIMER 1 which all use the same pre-scaler, so I dont know how 9 and 10 can have one frequency, and 11 have a different frequency.


Unless D11 is configured as OC0A instead of OC1C, which means that it will work off timer 0.

TCCR0A &amp;= ~(_BV(COM0A1) | _BV(COM0A0));
TCCR1A |= _BV(COM1C1) | _BV(COM1C0);
 ...
OCR1C = ...;