Have you tried deleting Firefly from the configuration menu and re-importing? It should ask you if you want the Aired or DVD ordering.
I have the same problem as others, but I will not mess up with that database file since it works for bigbew.
bigbew can you once more explain how you did it
Does the plugin recognize your Firefly series at the begining? I was changing the episode names couple times and it didn't recognize single one.