While I am not sure how to turn it off, your problem might be that you are not saving the values that were generated in the M303 command. This was a problem for me at one point.
Did you send an M500 command after performing the M303? If so do you have an M501 in you config file?
M501 will use the config override file, which is where the values are saved when you send an M500 after performing M303. Make sure M501 is near the end of config.g.