There is a good chance you map is corrupted. Try inserting it into another map bank/slot and then try again.
I was planning on just using my save file:p. Either way, I will try and give it a look right now.
Edit: So, I am playing with this and I have no idea what it wrong. My best guess, since no matter how much I play with the tiles, is that you forced a secret base open and you are missing the command which allows decorations that use tiles. What I mean, is when I changed the outside staircase, not the one in the basement, into the secret base hole thing that you use secret power on, and then I pack up the base, it doesn't close. I can still enter the base as if I made one, even after I packed it up. I believe it is the initial script which opens the base in the first place that is preventing the decorations from being placed properly.
Edit2: the script which opens a secret base in Sapphire is located at 0x1A2BE1. It uses a lot of specials which we have no clue what they do. Take a look at it.