Give the color to the eyes.

Basically two things comes to my mind for your problem.

1) Are you also resizing the alpha layers too? Aside of the main layer... They are important so that the layers and alphas blend together well.
2) Each race (Saiyan/Namekians/Buus/etc) has a different preset size for the textures. Also those with two genders are also different sizes between them. Male eyes are always smaller in size than female eyes (at least humans/saiyans which are the ones I've modded).
- If you are swapping eyes between races, you have to adjust the size of the eye, to the default preset size of the race you're going to apply it.
- If you are just resizing eyes within the same race, resizing the eyes for both, main layer + alpha layer, and making sure its centered to pic, should work. And also make sure the alpha layer is also being saved, when you save the eyes.

I hope that helps.

Edit:

This is speaking in Photoshop for the textures, that is... If you're trying in other 3D softwares, better someone else could try to tell you. ^^;