@trapdoor:
Have you tried to burn and load that modified image anyway? What version of GifExtractor are you running (afaik, the latest is V1.6)?

I've had the exact same problem with an older version of GifExtractor (GIFs not showing up after having been replaced,) but everything worked well when I burned and loaded that image anyway - well, that's been before I've upgraded to GifExtractor V1.6, though...