I think it might be in tga format which means it is probably flipped. You can verify this by using UTF Editor to open the Mat file. If the tga root says MIP0 that means it is a tga and FL only reads them correctly if they are flipped. In that case you can extract the file (Or use Milkshape) then flip the file vertical and resave as a .dds file (There is a plugin for Photoshop and most programs that I know of). Then reimport the file to the MIP0 Node and rename it to MIPS.