So for everyone that has been having issues with using the box injector, I was experimenting and I finally figured it out. It was a really silly mistake, but it does make a difference.
So, you download the boxdata information that was posted in the first post. Now you HAVE to make sure you use the code.bin with the boxdata.bin. YOU CANNOT USE the code.bin file that was downloaded to be used for the single file injection. So I would suggest making separate folders on your computer for doing single injections and whole box injections. You have to make sure you are using the right code.bin along with the right file. That is all everyone.
Edit: Also, I deleted the pokemon.ekx file off of my SD card as well when using the box method just to ensure that it would not get mixed up.