My 2 c...
If I'm correct, a Fast PWM mode is used, and PWM value is modulated to achieve more resolution.
Every time you change PWM register in Fast PWM mode, it will glitch. Unless you use Phase correct PWM mode on timers.
On 20 MHz clock, glitches are smaller, because of shorter time slices, but are same relative to clock...
I don't know if this is the reason but it might be worth looking into.
Regards,
Siniša