Ok, started mods on my spare board, first removed the auto current reduction circuit, found that the 50% decay mode seems to have improved the issues around mid-band resonance, but the steppers are noticably noisier ( hiss ), this is probably due to the low current switching frequency, looking at the TB6560 timing diagrams the internal osc looks like it needs to be substantially higher than the maximium step frequency, should also eradicate the audio hiss, I'm looking at using 330pf to up the frequency to about 130kHz, back later.
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Ok, tried that, much much quieter or at least I can't hear it ( cats may be able to though ), I'll setup two dial gauges tomorrow and try running a long program ( 1 hr ) just to make sure that I am not loosing any steps, I have not yet tried the 7414 buffer fix yet to square up the step signal, will only do this if needed to correct for missing steps.