Hi Ennech,
Choose a value for microsteps that your machine runs smoothly with then, within motor tuning, set the steps per unit accordingly and adjust the velocity and acceleration to suit. Once this has been done there is no need to adjust microsteps again unless you think that you can improve machine performance over your earlier setting up.
Check all your wiring for poor connection, especially the axis you are having trouble with and also check the mechanicals such as loose coupler between stepper and leadscrew (check all grubscrews for tightness) etc. etc.
I know you have probably already done all this but most problems turn out to be something real simple that has just been overlooked.
Hope this helps,
Tweakie.