This is probably not explained in the manga, because the manga is... well, not great.
Kaburagi Shisei's eyes are mentioned in the novel, though. On page 666 of the one-volume edition (book V, chapter 3; right before Hino Koufuu is slain), we have:
His unusually-large, almond-shaped eyes were limpid. His face was so well-sculpted, I might even have called him handsome - save for his bizarre eyes.
Kaburagi Shisei had four irises - two in each eye. They shone through the darkness, glowing the color of amber. That peculiarity was genetic in origin, and had been passed down the Kaburagi lineage for generations. They were a testament to the fact that his cantus was on an entirely different level than that of the common people.
So I guess it's just some sort of genetic weirdness in his family, probably a benign phenotypic side effect to whatever mutation makes people of his family particularly powerful PK users.