Most likely cause is you are losing steps, try cutting accel and Velocity in half and see if it helps. If it does then try increasing again until you have problems then back off a bit.
Also check for any rough or binding in the axis travels as that could also cause you to lose steps if your tuning is near the limit for your motors/drives.
It is not impossible but highly unlikely to be the software unless the DROs show the wrong movement, so keep an eye out for that if it happens again.
Hood