I can understand the side of luck, but they don't show up in NEI either. Can someone post the block ID number and I will see if i can generate them manually.
Actually, nm I will just do a block id dump right quick and check..
If they are at least in the game then they should be generating, maybe just an NEI bug. I will report back in a few minutes.
EDIT: Ok so the ores don't show up in the NEI Item/Block dump.. Ruby ore is listed in NEI as Block ID 213 and I do find it in the world naturally. I would suspect 213:1 / :2 / :3 etc would be the sapphire or green sapphire..
...
Did a bit more digging, literally, and came across the green sapphire naturally generated in the world.
Performed a 'block pick' and indeed Green Sapphire is ID 213:1 which yields a Green Sapphire gem, ID 5267:1.
So.. This appears to be an NEI plugin oversight the ores are being generated correctly.