I saw the issue raised by Dreadfred and answered by Gildor here:
Hi. Probably these blocks are transparent (has something encoded into texture's alpha channel), so your image viewer just ignores any color of pixels when displaying it.
Though it seems these 3x3 blocks aren't "culling" what's beneath the alpha channel (if I understood that correctly)
Sometimes exporting uncompressed TARGA fails, so my solution then is selecting 3x3 black squares in GIMP and resynthesizing
Just thought I'd raise this slight issue