Is it about the weird white line/tutti-frutti that shows up on your Flat? There's a simple explanation for that: Prime 2.0 made a slight mistake when he said "Doom Graphic Format". That is a column-based format that is used for wall and sprite graphics; what you want is "Doom Flat Format", which is a different format entirely. SLADE does make the distinction between the two, so just convert it to that format instead.
Also make sure they're between F_START and F_END marker lumps; I'm assuming they already are.