As you know Libreelec is an Small os for Kodi. Remote configuration only works with kodi. If we close kodi and run any program like Chrome, remote controller may don't work. You can play lirc / irw to reconfigure keyboard for work globally. I have nothing to do with your remote. You can use cheap wireless mouse / keypad like
I have several usb remote controls, and have the same problems with all of them. This is one of RC i'm using 1150107397_w437_h473_pult-mx3-air.jpg
I'm not fmiliar with linux, lirc is for infrared RC i guess? pls let me know if there's a simple way to configure usb RC