Yes I can't wait to grow my own corn and not have these issues!!Hope you don't mind me butting in on the poop problem...
Could be just just the change in water or even different bacteria in the soil.
On a side note, I also noticed a change in my IBS after quitting corn. I had quit eating eggs before I got chickens because they gave me such bad flare ups and outrageous gas... My girls get no corn and their eggs do not bother me at all... I miss corn on the cob, though, and I am thinking of growing a heritage variety. No one growing it near me so I do not have worry about cross pollination contamination.
I also find that bacon gives me bad flare ups. Oh how I love bacon.. but I just recently bought grass fed pork bacon. No corn. We shall see if that helps!