I had this problem too. My exported DDS wasn't 1024x1024! I didn't realize that GIMP wasn't exporting the entire canvas size, but just the size of the layer I'd been using, which was smaller than 1024x1024. I fixed it pretty simply by right-clicking the layer and using the Layer to Image Size tool. Then just export the DDS as usual (using BC3/DXT5 and generating mipmaps).