I'm back. I've gone a bit further in my experiment and reinserted a background after filtering it. Here is the result:
Horrible, right? Well, let me explain the image a bit:
-There are some artifact (like the brown block where the stairwais should be) caused by my buggy loading routine.
-Some colors are wrong because of my poor saving routine. Currently it doesn't even add new pallettes. It just fills the empty colors found on the pallete and, when there is no more room for new colors, it reasignates the closest colors.
-There are some black squares. I don't have a clue where they come from, but I suspect I can find about it looking at LGPTools source code (because they are there if I preview this field there).
-The image overflows the screen. Obiously, because I don't know yet how to disable the pixel doubling (if someone told me how to do it, I'd be happy).
Anyway, the point of this image is showing that filtering the backgrounds is possible even without modifying the engine (well, just enough so that it draws the tiles smaller). The image won't look cracked as long as you apply the filter to the whole image.
By the way Synergy Blades, I think the reason why your backgrounds crash the game is not at section 9. I think your problem is at section 4. If you make it too large (adding too many color entries), the game crashes as soon as it tries to load the field. This is the reason why encoding images in the FF7 format is painfully hard.
Oh, one last thing. I found one more error at GEARS (in both pdf and wiki). There is a 4-byte field called nbColors. I don't know what it conatins, but I'm completly sure it's not the number of colors (at least not at that exact offset).