I am not sure when this behavior changed, but I am now consistently able to restart or shutdown my MacBook Pro using L6 and 10.10.
NOTE: A warning still pops up, but if you leave it alone, the sync will finish and the computer will shut down.
Yes, I just noticed this last night when I shut down. Same as you—gives a warning, but if you leave it, it shuts down.
Now I have to break my habit of quitting Logos and then shutting down my iMac!
