I have found a hot fix for this bug, but it's ugly.
The problem is that it always boots in VGA mode after a DVI session. Later on boot process - if you are lucky - it will switch to the selected user HDMI resolution. I think the initial VGA mode is the reason for a bad detection of HDMI modes. Not all possible TV resolutions and/or refresh rates will be found.
A "Soft Reset" or a "Hard Reset" made from the system settings menu will not solve problem - initial VGA mode will stay.
The only solution for me was to rewrite my MicroSD card with a new LibreELEC image. That will make the initial HDMI boot resolution (720p / 50Hz) work again. All possible TV resolutions and refresh rates will be found, too.
Maybe somebody should report this as an official bug.