I have a similar problem with my Cubox-i4x4. I use 1080p 50 Hz as my Kodi resolution. After first power on, it works ok. After I turn off the TV and amplifier once then turn TV back on, the TV detects 720p resolution for some reason, even though Kodi/Cubox is still outputting 1080p. To fix the problem, I have to go to System settings, Video section, and change resolution or refresh rate then change it back. TV then detects the correct resolution.Cubox is connected to amplifier by HDMI which outputs to TV over HDMI.
Last night I made a change to settings that may have fixed this problem for me. I need to test it more to be sure. In Settings->System->Input devices->Peripherals, I have two options: CEC Adapter and generic_video,hdmi_video. When I click on the second option, it brings up a menu with only one option: Detect hotplug events. Up to this point, this setting was enabled. I disabled it last night and so far after several on/off cycles of the TV and amplifier, the correct resolution is detected by the TV and outputted by Kodi.
See if that works. You can also try playing with CEC Adapter settings and the setting that updates available video resolutions (forgot where this is).
I'll give it a try. Thanks for the hint.