The Auto Log combat in a raid instance does not work for Onyxia's Lair. MC, BWL, and ZG all work fine, but I always have to manually log Onyxia's Lair.

My only guess is that the addon checks to see if you are in a raid instance every time you change sub-zones, and since the sub-zone outside Onyxia's Lair is also called Onyxia's Lair it doesn't know that you changed sub-zones after zoning in so it doesn't see you are now in a raid instance and start auto logging. This is just my guess, I don't know for sure.