Had the same problem with a tv show.
But this is what I saw in the Complete my
Season FAQ section:
"Note: if you previously purchased single episodes from a season, and the Complete My Season price will be less than the current price for a single episode, you will not be able to purchase the remaining episodes using Complete My Season."
So it is their policy I Guess, although unlogical.
The above reply is correct. You should have purchased complete my season when teh balance would have been more than the cost of each episode which would have been at least $2.99 since the HD episodes cost $2.99.
If you want the rest of the episodes, you'll have to either buy the whole season of individual episodes, whichever is cheaper.
The final season had some great shows.