Sounds like you are losing steps, especially if its ending up lower than it should, try reducing the Accel by half and see if it disapears, if it does then you can try and fine tune from there.
Entering a number into a DRO will just put that as the position, you can add and subtract from DROs now so for instance if you were 0.250 too low you could subtract that from the DRO and when your code runs it would move the axis up to where you should be. You can also enter commands in the MDI line to move an axis or if you want to move by a set distance you can set the Step Jog DRO to what you want to move and set the Jog to step mode and each time you press the jog it will go that distance.
Hood