The point I'm trying to make is to test and find out which axis is actually causing the problem.
I don't believe it is an encoder, as they tend to be go, no go, either they work or they don't.
for unusual encoder probems, scratch on disc,or loose encoder coupling,or intermittant wire contact you would get loss of pulses and and accuracy/repeatability problems. Most Ac drives will fault if total loss of encoder feedback, so don't think you problem is there.
If the control will display axis lag or following error, (option in some set up pages).
Manually jog each axis at a slow feed rate and see if each axis comes back to o.oooo when you stop jogging.(following error will be greater the faster you move).if one axis does not come back to o.oooo, probably is the problem axis. It may be right at the edge of the controls allowable "in position" range. Why the problem is intermittant, most times it is in position, every once in a while it isn't.
If you find one axis as described, check the manual for the servo drives, for adjustment procedures. Of course I am assuming that mechanically the machine is okay. A sticking gib or other mechanical load can cause in position problems at lower feed rates.
Al