Ok, so a single card runs fine as an auto-detected configuration. Is it possible that one of the cards is misbehaving? Can you try each card individually?
Each card on their own works fine with the original (automatic) xorg.conf.
That could very well be it, the somewhere else part. Did you try to move the VGA/DVI connector to another card, or to another port within the card? It could be that the autodetect is using the card that has the monitor on it, but then with =all it is using some other as main screen in a broken multi-screen config.
Ya almost seems like some broken multi-screen thing to me?
Do you get the ubuntu splash screen before it turns black? Can you SSH in to the machine? Does the numlock still turn on and off?
Have you tried booting with
nomodesetNo splash screen, complete black screen with led signal on monitor. I doubt I can SSH in. Numlock does NOT turn on/off.