Unfortunately WDW doesn't make it as simple as "drop a night" -- the adjusted dates must be available as a "new" reservation in their system or you can't get the same promotion. It sounds like that's what happened. Your original booking was for free dining, and when you dropped a night, the adjusted dates were no longer available as a new stand-alone reservation in the free dining pool of rooms. So sorry that happened! For future knowledge, sometimes you can call and get a Guest Services manager to help preserve the promotion.
Are you pricing different promotions or the same promotion across each of the different time periods? Different promotions can and will make a difference, as you found with changing your original "free dining." I believe there is free dining as well as a room-only discount, as well as standard rate room-only and package. And as PP mentions, the ticket prices adjust based on your dates. And I believe free dining requires a hopper, but other packages may not. So there's a chance you've got some apples-to-oranges comparisons.
Good luck with the figures and enjoy your vacation!