So I was working on a ambient light filter for IR receivers and using the BP PWM mode as a signal generator, turns out the PWM mode won't give a 1% duty cycle, is this a hardware flaw or software setup issue?
The duty cycle resolution depends on the length of the period. There's a formula in the datasheet to calculate it.
Expanding on that a little - at very high speeds there may only be 1, 2, or 3 bits of resolution. If the PWM period is only 2 clock cycles, then the duty cycle can only be 0% (0 clock ticks) 50% (1 clock tick) or 100% (2 clock ticks). If this is the case, the Bus Pirate PWM calculator (which uses integer-only math) will round down to 0 for any values below 50%.