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(Get the code!)
Trying Kazabubu's suggestion to extend GdmXserverTimeout cleared it up for me. At least it's been fine for the last week plus, I've rebooted many times.
Okay, here's my hypothesis of what's going on:
1) Note that Rami said boot was slow for him until he turned off AHCI, and then when he disabled it boot sped up and the problem disappeared. The AHCI-slowing-boot thing sounds like some weird BIOS/kernel interaction, but note: auto login didn't work when boot was slow.
2) The system I'm experiencing this on has a very, very slow old hard drive (5400 rpm 1/3 height 40 gigger from like 7 years ago), so boot is always slow.
3) I'd noticed that when this problem happens, X would start coming up, then it would go away, the system would go back to the console, X would start up again and get to the gdm login screen. Like I would expect to happen if the gdm script was timing out, killing X, and starting it again. It probably didn't time out a second time because the system was no longer as busy with processes starting up in the background.
So the next thing would be to look at the code and see if gdm still honors the AutomaticLogin after having timed out once. If not, there's the bug, and it's going to be more relevant as efforts to parallelize the boot process continue.
Steve