Calibration, chain length issue

Have a problem with calibration. With tape measure distance between motors are about 3500mm, with automatic length calibration 342.01. After chain length adjustment pin inserted in second hole, then I say to sled go 550mm down in reality it goes 548, then up 550 - reality are 539, sides from center 550-551. Tryed to insert pin in to the first hole, but measurments are more far away from reality 550-530 center-top. So the best measurments are then pin are in third hole center top 550/548,5, center-bottom 550/549, center sides 550/550. There is problem? I missed somthing in calibration? Is way to do thine chain length adjustment? Or sprockets was not ideal leveled?