I'm thinking it is the encoders more specifically the roller bits. Sometimes bits of crud can build up, clean them well and the frame itself.
Does it happen in one spot on the frame? My friend's system had some damage done to the rails when she moved it with the "help" of her daughter, they bent the center support area and it would always skip stitches there, we took it back apart and put the ends together in the middle for the frame and that helped quite a bit.