What firmware are you using ?
On v1.0.53 for sure most of the PWM frequency options in MegaTune run the stepper at a low frequency (10hz ish). The duty cycle control isn't very constant and this causes the stepper to jump about. However if you pick a PWM value which is a multiple of 64 (0, 64, 128, 192) then the output runs at 1.2KHz and the stepper movement is smooth. Give it a try.
Hilly