Hello.
I have the latest LibreElec version (8.2.5) on a Raspberry Pi 3 and I have exactly the same problem as OP bogard.
My problem is that, strangely, the "HDMI port number" isn't among the CEC options. Here you can see it:
(here with less resolution: https://imgur.com/a/g7mxlwb)
Why does this happen? I think that would be the solution 
Thank you!