consistently? or intermittently?
i have no mimaki experience, but, if consistent, you should be able to perform calibration, to correct this
if intermittent, some sort of encoder strip issue? clean GENTLY with the proper solvent, isopropyl, i would think.
clean the sensor as well. make sure it is not misaligned & think carefully, was it cleaned recently with THE WRONG SOLVENT?
look at a service manual & see if there are calibrations related to the encoder.
the rolands couple the encoder through a cut carriage cable, if mimaki does the same, this would be highly suspect. sorry i have to respond with nonspecific advice, but, it's all i have