Apparantly a lot of people have troubles with this, since Google is completely filled with these command mode settings.
See page 22 and 23 of the manual.
I found this to resolve the issue:
It depend of how to remote is set currently. DVD 3 is the default setting. If you changed it to DVD 1 with the menu of the RDR-GX360, it mean the remote is still in DVD 3. To be able to put it back to DVD 3 you need to take back control of the unit, that mean putting the remote in DVD 1.
To do that you press enter on the remote and hold it, at this time press "1" on the remote, when at least 3 seconds have elapsed you can let go the 2 buttons.
You will then have the RDR-GX360 and it's remote paired again. At that point you can let it that way, or if you have infrared interference with other equipment, you can do the same you did to put it back to DVD3, starting with the RDR-GX360 and then pressing enter and 3 on the remote.