I have tried different things now, but I still can't get this to work. I downloaded an Aloha repaint (fsx_p3d_aloha_airlines_737-200_1970.zip), which is painted in DXT5 format, and supposedly tested in FSX-SE. The only thing that shows up are the wheels. I also tried the batch script presented here, converting everything in the standard TinMouse liveries nicely to DXT5 with mipmaps, but still only the wheels showing up. If I try to disable 'Preview DX10' the textures show up in the FSX menus, but the whole sim crashes when I try to load a flight. So, another blind alley there of course.
This is such a weird problem. Are there some other textures I need to convert as well? Some transparent TinMouse textures that for some reason are on top of those I try to use, and therefore turns everything grey? I suspect something like that since only the wheels are showing. They were invisible (not even grey) before, so maybe the grey stuff wont affect these textures.