I'll throw another vote in for stalled steppers.
As mentioned, increase the ramp up time(acceleration) and decrease max step rate.
Note: no experience with Bartelising a scope or using his software(except for a casual look at it a few years ago) but plenty stepper experience(CNC).
Also, have a look around for better steppers, most steppers can handle a few hundred RPM no load and much less when loaded, sadly people accept this as the norm, but there are newish chinese made steppers that get up to 10,000 RPM(!) no load, and still handle over a thousand RPM when loaded. Very popular with the CNC guys. Approx $50-$80 each depending where you get them, plus extra spent on beefing up your power supply.
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