There are two different kinds of eggs. One is the normal egg - cream with light green spots. Then there is an irregularly blue egg with a red circle in the middle. This egg was only obtainable from Pokemon Mystery Dungeon and it only contained Manaphy.
So, the colouring off the egg will not be different. Unless you have applied a method (e.g. Masuda Method) or a hack, or you possess the Shiny Charm (Gen 5) then the chances of a shiny hatching out of an egg is 1/8192. The egg will not be another colour.
Hope I Helped. :)