The Deal of the Day is its own list. It doesn't pull from existing prices and then discount it further. When I set up the prices for the Elixir Sale, I neglected to look at the Deal of the Day list. I did remember to get the Elixirs from the Guild halls and on Vinnie though

Thanks for taking the time to post a note and our apologies for not making the Deal of the Day items match up with the sale.