I hadn't gotten around to checking for .MIMs in the iso yet, Vehek. I *believe* Yazoo's tools may have used LZSS decompression on the room files, and the .MIMs are also LZSS compressed, aren't they?
After a quick check, it appears the compressed .OUT files in the Rooms directory may have 3D data first, then the palettes and textures, etc. The "drp" data comes first in these compressed files, anyway.
And as far as 3D data is concerned, since we're talking about 2D pre-rendered backgrounds, wouldn't the only 3D data involved just be walkmeshes? Do you remember if .MIM files include walkmeshes along with 2D pre-rendered background data, Vehek?
And a follow up question to Ramsus and Zeality: are you pulling palettes from the .act files or from the "#palette" file that's also in the Code directory? I've found a workaround with Tile Molester now that Ramsus has revealed the palette offset, but I used the #palette file and it looks just a bit screwy still.