The drives say they are differential input, you could try connecting them single ended if you wish, info is in the CSMIO manual I linked to.
However you said things got worse when youdecreased the microstepping, did you ever try that microstepping on the other controller?
I cant think what could be causing that but if you attach your xml I will look at it to make sure there is nothing wrong in it that could possibly cause something like your problem.
Hood