[Kendos]

With "Use Full HD HDMI modes for 3D" disabled does it work every time, or still fail?

Can you first add hdmi_force_hotplug=1 to config.txt (and reboot). Not expecting it to fix anything, but removes a variable in the following tests.

A couple more experiments may be interesting. If you play the 3D video and get a blank screen. Can you:
Power the TV off and on again. [still blackscreen]
Change AV input away and back with remote on TV [still blackscreen]
Power the receiver off an on again. [still blackscreen]
Change AV input away and back with remote on receiver. [still blackscreen]
Unplug and then replug hdmi cable from receiver to TV. [will try]
Unplug and then replug hdmi cable from Pi to receiver. [still blackscreen]
Unplug hdmi cable from Pi to receiver and directly connect it from Pi to TV. [still blackscreen]

Do any of those make the picture reappear?

Can you also add "config_hdmi_boost=7" to config.txt (and reboot). If that doesn't help try "config_hdmi_boost=11".
I don't think that will help, but it's a simple thing to rule out. If it doesn't help you can remove it.

I will try the settings in the config.txt tomorrow (its already 11PM here).
But some testing I had already done (see above in the quote) and yes, with "Use Full HD HDMI modes for 3D" disabled it works everytime.
I will do tomorrow the same with the settings.

How big is the disadvantage to disable omxplayer?
Because with omxplayer disabled the movies started with no blackscreen but I will do more testing tomorrow.