Insofar as the pink one goes.. WA seems to recognize only a particular set of colours. Particularly on the purple and cyan-side of things there isn't much to go with.
If you want it to be more purple, make it a lighter shade of purple and see if that does the trick.
Skynet shows up as a mess in my game as well.
Not sure how to fix it as I don't have PSP installed, which I used to use to make worms flags.
Have you tried creating a new plain BMP-image and copying the skynet one into it?
Also, just a tip in general, it's sometimes good to pixel-edit the image. The supersmall size makes images hard to make out. Sometimes I emphasize aspects to make them stand out better (i.e. make blood drops bigger and brighter red), same could be helpful with the skynet one (less stripes / bigger ones, and make the red brighter)... who knows, this may even fix the visual bug.