There's a chapter in "
The Antietam Effect" that discusses why the rebels had major problems.
The tale starts with the 1861 eruption of
Mount Dubbi, the largest volcanic eruption on the African continent. The Mt Dubbi eruption threw up huge quantities of matter into the atmosphere and massively disrupted global weather patterns. A few months later the
California megastorm resulted. The unusual storms continue, and disrupt British reinforcements during the Trent Affair. Even in mid-1862 there is still residual disruption to the weather that compromises the Peninsula campaign.
One of the effects was that the harvests were poor. In the area of operations of Bull Run the harvest had effectively failed, and there was a major disruption of food supplies, as Lee was expecting to find harvested wheat in the area. Even before they crossed the Potomac the troops with Lee were suffering serious malnutrition. When they found food in the fields at Maryland it caused dysentery - when malnourished for a prolonged period the GI tract becomes unable to absorb nutrients, and hence when the troops gorged themselves on animal feed corn it went straight through them.
Now, DH Hill's and McLaws' divisions arrived they'd been regularly fed with army rations and hadn't started to succumb to malnutrition. They ate the corn fine, and didn't suffer from dysentery much.