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Microstepping and steppers in serie skipping (tmc2100)

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Hi
In an attempt to get smoother surfaces and less noise from my Folgertech FT-5 (MKS Gen 1.4, Cartesian with two steppers for Y axis) I have replaced the stepper controllers with TMC2100.
This take the 1:16 from the MKS and make it 1:256 in "spread cycle" mode, which was was very nice for a few minutes, until the Y axis started skipping.
I have tried changing the voltage from 0.9v to 1.5v, with no result.

Is there anything fundamentally incompatible between twin motors and micro stepping? I have considered changing the machine to corexy, but that is a lot of work just to get microstepping working, beside I need it working and plan do make a custom corexy next year anyway. Should I abandon and do with the noise and rice paddy surface?

Thanks for reading!

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