my best guess is the height of the room. i dont think the glass is the problem. i've used stone and dirt to cover up the water and the crops have always grown. lighting is enough as long as the seeds dont pop out after initial placement, then ur good.
Actually, wasn't Glowstone changed to counting as transparent in the latest version? I know you can't place torches on it any more, and I've heard that you can now put it above chests (and they'll still open).