JDoom and DeepSea editing

I'm attempting to create a wad in DeePsea for JDoom, but when I try to test the level, it won't test cause it tells me the pallete overrides the origonal game pallete. I did make some changes, but they were nescessary. I also tried to make the wad load manually thru JDoom, but it wouldn't load at all. Does anyone know how I can make my wad work, with my altered pallete? or how I can make the pallete bigger? Or is there some kind of trick I can use to squeeze more colours out of the Doom pallete with JDoom? Any help would be appreciated.

I don't think you can tinker with the games color palette without killing it.

I would belive that, but when I used this level (or rather what is done of it now) in JDoom 1.0 it worked. But I want to use this with the newest version of JDoom.