From what fritsch told me it's an issue with some newer video drivers that are in the kernel now. I tried recompile libreelec with older kernels without any luck, so I'm now on ubuntu where it's much easier to change. In the next couple of days I'm going to attempt kernel 4.7 (which should be broken) and then provide some debugging info to intel. I wouldn't have high hopes though... last time I ran into a similar issue they told me to either use the old kernel or buy a new cpu.
Looks like this issue will never be fixed, since it only affects people with a very particular hardware combination: an Intel GPU + a Denon AVR and syncing TV refresh to the video...
Several months and this problems happens build after build.