Hi,
the jitter problem turned out to be caused by the DRV8825 stepper driver. 
Actually it just looked like jitter in the step generation. The driver 
could not drive the motor properly when set to low  current (300 mA) at 
certain step frequencies (around 200 steps per second) in full step mode. 
After I sett the drivers to 1/8 microstepping the problems disappeared.

So far so goo, now I'll start looking into controlling my stepper motors 
from a Python script.

See you
Flo

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