PWM/DC-Motor Control: Pins 5 and 6 (sounding) slightly slower?

I'm using the Arduino's PWM pins for controlling a brushed DC-motor with a L293D H-Bridge driver. When using PWM pins 5 and 6 the motor runs slightly slower than if either one of the other pins where being used (at least of what I can notice from hearing).

According to this TimerPWMCheatsheet pins 5 and 6, the slower ones, are driven by Timer 0, the others by Timer 1 and 2. Timer 1 has a smaller duty cyle of only 256, compared to 510 of the others. It also runs on a higher frequency of 976.5625 Hz instead of 490.20 Hz. Is the difference in these parameters the reason for the motors behavior? And if so, why?

Thanks for your help!
section “Notes and Warnings”