it seems to me you're subject to different waveform coding, with arduino mega look at fast PWM versus phase correct PWM but also frequency & phase correct PWM. The last 2 cases will divide by 2 the actual timer frequency generation.
I've quicked look on SAM3X... datasheet for the equivalent story, same except they use WAVSEL to choose whatever mode. Later on the datasheet, they also speak of center align or left align.
So there is no bug, just program correctly the registers...