I just did this yesterday.
I used a code to book our room. When I booked, I was within the 45 day mark. Since I didn't have the money on had at the time to cover the package, I just booked room only. I called yesterday to add dining and passes and pay the balance on the room.
The first CM told me I could not keep the room discount and add dining. I knew this was wrong. I've spoken to several CMs that told me it could be done. One even gave me the code they have to enter in order to allow you to keep the discount when you upgrade to the dining package.
The CM said I had the right code but the system would not allow me to keep the discounted room rate.

Since I wasn't getting anywhere with her, I hung up and called back.
The next CM was able to book it with the discount. It took about 30 minutes to complete the process, but I was very happy in the end. She had to cancel the first reservation then rebook with the plan. I must have asked her 10 times if I'd still be able to keep the room discount once she rebooked and she said yes.
It took awhile, but in the end everything worked out fine.
As far as the $1000.00 difference, the CM may have plugged in the premium dining plan instead of the other one?