I'm not exactly sure what's going wrong with atvclient (no hardware to test, LE is shipping latest atvclient version with krypton patches), but I noticed that kernel support for the apple ir receiver was disabled in LE.
Here's a test build with CONFIG_APPLEIR enabled:
LibreELEC-Generic.x86_64-8.0-devel-20170616093132-r25705-g16fea8734.tar
Could you please test this build and report back if this works better/worse with atvclient running?
With added kernel support kodi should now receive IR events without atvclient running. To test this disable atvclient:
systemctl mask atvclient
and then reboot. (you can later re-enable atvclient with systemctl unmask atvclient and another reboot).
In both cases please post kodi debug logs where you press some buttons.
Also please post the output of the following commands:
lsmod
lsusb -v
dmesg | paste
lsof | grep /dev/input
BTW: the kernel driver only supports the remote codes of the original Apple remotes, so please test with these (maybe the Harmony configured as a Apple remote works, too). Other remote codes should be supported by running lircd, but let's leave this for later.
so long,
Hias