I might be having this same issue, but I would like to check that an additional complication isn't getting in the way.
My amp is at the heart of my system, with the TV and Pi connected to it on separate ports. Video and audio playback from the Pi works OK, but I can't navigate menus using the TV remote (been using a mouse to test). So my CEC commands needs to go from my TV, to the amp and finally to the Pi. Should this just magically work if CEC is enabled and I've selected the Pi input source on the amp, etc? (CEC control of the amp is working OK). Can someone confirm that should all work OK? Thanks.