Hey guys, I think I found the REASON and SOLUTION for this issue, at least for me. I'm running Yosemite, clean install, FileVault, 2012 rMBP 15". I've had no login problems at all since first day clean install. However, last night I did something and this morning, I could not restart or shut down from the Apple menu. So what did I do? Mess with the wallpaper.
I was using the default Apple wallpapers, and decided to add a Folder. Fine. I then created a Wallpaper and dropped it in the folder, and switched to it. Everything seemed fine. Then I created a second wallpaper, put it on a 5 second timer so it would change, etc. So this morning I went to restart, but couldn't. I had to hold the power button, as I got a black screen with only my mouse. So I restarted with the power button, then tried to shut down. Again, black screen, mouse visible. I booted from a Yosemite USB drive, repaired permissions, repaired disk, etc. No errors. I booted back to my SSD and noticed something. My custom wallpaper was not the blurry image I was being shown at the login screen. It was the default Yosemite image, but it looked like it was a bit pixelated, and not the smooth blurry image you usually see.
So I logged back in and again, tried to restart/shut down, and to no avail. So I tried resetting SMC, PRAM, etc. Still nothing. So I removed all the files from the Launch Agents/Daemons, like someone suggested, etc. But nothing seemed to work. Then I went and set the wallpaper back to an Apple default wallpaper. I logged out first, then restarted. It worked. Then I logged back in, logged out and shutdown. It worked. When shut down, I reset the SMC and PRAM again. I logged back in, changed my wallpaper back to my custom wallpaper.
It was now I was able to go to the Apple menu and restart and logout. AND maybe the most important thing now, on a cold start and restart, I could now see my custom wallpaper as the blurry login wallpaper, and NOT the apple default wallpaper. I'm almost positive the wallpaper issue was my reason, I've been using Yosemite since day one without any logout/login issues. I start to mess with wallpaper and bang, the exact issue you guys are having.
If anyone wants to give this a try, I would like to hear if it worked. I just lost about 2 hours this morning trying to figure this one out. I'll post back if it comes back, but I'm not changing my wallpaper anytime soon...
Bryan