No, you are not limiting current, Half current only applies to when the motor is at a standstill, it then drops to half current after a period of time to reduce motor heating.
You said before that the machine has been working fine so I very much doubt it's a motor tuning issue which is one of the reasons for asking about the Micro steps.
However, if you have changed the motor tuning then this would cause missed steps if you have the motors over-tuned.
So if you are 100% sure it's not mechanical or electrical then you could lower the motor tuning and it will most likely go away but in my opinion, but seeing as it was working fine before, this could just mask the real issue.
Give more info on the motor tuning and the controller being used so it will give us a better idea if you are over tuning or not.