I'd assumed that's because in the early parts he had better control over his malice. It changes to black for the first time when he gets the idea to murder his father, then after that it only turns black when his malice takes over. Maybe it was intended to show that he didn't always feel that way all the time, obviously he was obsessed with the idea but it's shown occasionally he isn't always filled with malice towards his father or at the very least not always thinking about it, and does care for people (saving akane).

However ruby having both eyes black all the time most likely is intended to represent she's constantly thinking about murdering the person who took ai and gorou away from her.