#1 - March 18, 2008, 9:35 a.m.
There was an issue recently where the bonus honor gained from the daily quest was being added to the estimate each time your character changed zone after having completed the quest.
If you are in and out of battlegrounds all day and complete the quest early, this means you are seeing about 400 honor being added after each battle but you won't actually get that amount.
I'm not sure if that issue was resolved, but with the changes coming in patch 2.4 it should not be a problem for much longer :)
If you don't think that is the source of your particular issue, I recommend you contact a Gamemaster through the in-game support system for further assistance.