Hey, Billy. My guess is that the X1 is programmed with the code for the "Power" button on your Yamaha remote, versus the "Standby" button (or maybe it's the other way around). If you hit the "Power" button on your original remote, can you turn the Yamaha back on from the remote? If so, can you turn the Yamaha on by hitting the "Standby" button? It has two buttons for a reason, and I have this vague recollection of one of my past receivers (could have been my Yamaha) needing to be powered up from the front panel if I hit the wrong power button on the remote.
If there is more than one set of codes for Yamaha in the X1 manual, I say try some others to see if they work for you.