Do emoryi crosses do better because emoryi are hardier or just because so much "new" blood is being introduced? I suspect a lot of "corn problems" are due to overbreeding and breeding only for morphs/color. Perhaps introducing wild caught corns such as the Carolina corn would have the same effect. Sure, your emoryi crosses will always be stouter but that doesn't necessarily mean they are any healthier than a corn with a more lean appearance. Just like a Lab may be no more hardy than a Husky.
Could possibly be that too.. Of course, when i make a purchase for future breeders etc, I do keep that in mind and look for stock that is likely unrelated.... Seems to have helped the difussed lines to be outcrossed too..