When this check box is checked, the ECU will only respond to the ECMLink application. It will not talk with OBD2 emissions stations or OBD2 scanners or factory scan tools or any other factory mode communication mechanism.
If you plan to take your car into have it emissions tested and they need to connect to your ECU with an OBD2 scanner or if you're trying to connect to the ECU using something other than ECMLink, you will need to clear this check box.
Once cleared, you need to turn the ignition off and wait for the MFI relay to click. Then, the next time you turn the ignition key back on, the ECU will default into factory mode (OBD1/OBD2).
This will remain true until you connect with ECMLink again. Once you connect with ECMLink, the ECU will remain in ECMLink mode until you cycle the ignition again.
So it's important not to connect with ECMLink before driving to the emissions station, for example. Or if you do connect with ECMLink, you need to make sure you shut off the ignition, wait for the MFI relay to click and then power it back up before they try to connect with the OBD2 tool.