i wonder is it because it is scalable in eps, so there is always some pixel tolerances when it generate to different size?
Double check the size of all objects to confirm it has no fractions in pixels. Fractions on edges become white or transparent pixels.
If scaling is involved then you need to be sure the new size will also be a whole number with no fractions. A 10px object scaled 25% percent generates a 2.5px object that renders as a 3px image with one of the pixels being a mix of object color and white or transparent.
The easiest way is the one that helix7 already told you. Make it larger and crop.