Because you say there is a needle hole and the skip is due to the needle not picking up the bobbin thread, I would rule out the encoders immediately. I would suspect your needle bar height isn't quite right or the needle is not in correctly. You probably are not out of timing because it would be happening a lot more than "occasionally" if it was timing. Do you notice it a lot more going in any particular direction like when moving the machine away from you or right to left?