The command sent to the firmware should be the same for a Move Absolute to (0, 500, 0) as it is for a Move Relative (0, 100, 0) from (0, 400, 0). You can confirm that they are the same by enabling Firmware SENT logs in the Logs page settings menu and watching for Debug 3 logs.
If you have encoders enabled, they will update FarmBot’s current position with the actual position achived instead of assuming the position based on the coordinate sent. So if the motors only made it to (0, 397, 0) and you send a Move Relative (0, 100, 0), the target coordinate will be (0, 497, 0) instead of (0, 500, 0) as it would be with a Move Absolute command. You would be able to determine if that is the case by watching the Firmware SENT logs. Some refinements to the motor settings may fix the issue if it is.