Confirmed, issue shows when there is a microcode update. I will rebuild without the patch.

Actually, my mistake, just used the wrong patch.
Upstream wanted 2 microcode patches tested, first one worked, second one caused a hang on intel microcode updates. While testing this for 4.6.0, I never uploaded the kernel build with the latter patch, now missed disabling this one and going back to the correct.
Rebuild with the correct patch will be up shortly.

After update (linux 4.6.1-2-next) both two, system boot and intel microcode are working

20 days later