I always thought that her eyes were just made to look way more blue because of a night filter they used. I actually used the dipper tool in photoshop to see how the night filter in the ending scene affected some of the other colours. Celestia's choker for example, is waaay more blue and has a darker tone in that scene than in a standard day scene.
... BURN HERETIC. HER EYES WERE RED BEFORE YOU BOYS SHOWED UP AND RUINED THE PARTY! CUPCAKES BE MADE OF YOU! RAWR! ... But seriously, I hope the magenta craze doesn't overtake the red Vinyl. I have grown rather attached to the eyes... I know, it is stupid, but I can't help it. Frankly it is driving me bonkers. It is like Derpy all over again. *Sigh* I sincerely hope they make red eye Vinyl Scratch official. Otherwise I might be tempted to troll the remaining red eye vinyls to death till they submit and assimilate to become pink.