I the same symptom on my Delta caused by extruder motor noise in the end stops.
In Repetier at least this causes the current move to end early and the machine looses position.
If you are using Repetier try:
#define ALWAYS_CHECK_ENDSTOPS false
In Repetier at least this causes the current move to end early and the machine looses position.
If you are using Repetier try:
#define ALWAYS_CHECK_ENDSTOPS false