I have set up a new Raspberry Pi 3 with the latest OSMC (2017.07-1), and I had it working with the remote control. I left the room for several hours, and when I came back the screen was black and the machine unresponsive, so I rebooted it. After reboot, everything seemed fine, except the remote no longer worked with Kodi.
If I stopped the mediacenter service, and tested the remote with the “mode2 -d /dev/lirc0” command, I was getting the usual series of space and pulse signals OK. And in My OSMC, the correct conf file was selected for the remote.
I compared the remote against my old Pi 2, and it was continuing to work there, so the remote itself was still issuing the same sequences.
I’m not sure how to proceed to investigate this further.