Even if you have a ton of lighting rods, it's possible to still loose crops to a lightening strike. You should see a dead plant in its place. If your crops are straight up missing, put a scarecrow in one of those spots and see if that fixes the problem. The scarecrows have a weird overlap, and sometimes little areas are unprotected. I think the rarecrows might have a slightly bigger protection area, but I'm not certian on that. The deluxe scarecrow has the biggest area of protection. If the crops still vanish right next to a scarecrow, then its definitely a bug.
