You almost always get one that is slightly slower than the other. Is there a huge size difference between them? If so you may have to eventually seperate them until they are close to the same size. I doubt that your little guy is too slow for guppies. He is either getting some when your not around or just not interested in them. What else are you feeding?
You could try feeding with tongs to make sure everybody gets their share. I had to do it a few years ago for some salt water fish I had.