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Its good to know that I am not alone with that problem, I spent half the day with this.
I have the same Hardware as GodfatherUr, TOM Mk6, 3 mm ABS . Just checked: I also have the older Makerbot NEMA17 Motors (VRef=0.6V). BTW the accelerated Jetty Firmware (pre Sailfish, with SF35) is working fine on my TOM.