Ryan,
I too have a 'granite' who has thrown two bad clutches. Each clutch went full-term, except the hatchlings were severely deformed. Although I did not pair him with a YB, rather a normal this year and a cinnamon last. Another thing to add, I too made the mistake of using Perlite with miracle grow. However, I have had 5 clutches hatch thus far this season, and it was only the clutch he sired that did not survive, the other 4 hatched pretty smoothly (other than some kinked caramels).
I am not sure if it is him, the gene he potentially posses, bad luck, or a combination of the 3.
Below is a picture of the granite sire...
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