A lot of people notice that when they cut out corn, they feel better overall...and begin having much more severe reactions to things that only used to bother them a little. It makes it look like cutting out the corn has hurt them in some way.
Here's the thing. If you're allergic to corn (or gluten) then you've been ingesting something you're intolerant to at almost every meal for most of your life. Of course, your intolerance or allergy has probably developed over time...but throughout that time period of intolerance, your body has essentially been a battle zone.
So imagine a battle field. Things suddenly calm down, the enemy just...vanishes. Are your soldiers going to take a nap? Of course not! They're going to band together, and go on high alert, watching for intruders or any sign of renegade activity.
And, seeing as there's very little to attack when you've cut the corn out of your diet, there are a lot more 'soldiers' available to attack any perceived threats.
When your body attacks a perceived threat, you feel rotten. It's a defense mechanism, digestive issues are your body's way of flushing a toxin from your system. Rashes sweat a toxin through your skin. Swelling increases liquid to make it easier to flush that toxin through. Except, of course, that food isn't really toxic.
Eventually, your body will calm down. It'll stop attacking those invaders. The SCD recommends a broth diet to jump start your allergy free dieting because it gives your digestive tract and immune system a chance to calm down and adjust. I think that's a great (though not always plausible) plan.
At any rate, if you are diagnosed with an allergy or intolerance and start noticing worsening reactions, don't despair. Take it easy, eat lightly, try to rotate foods so that you won't inadvertently create a new intolerance, and eventually your body will relax and (hopefully) slip into "normal" mode. A newer, healthier...BETTER normal for you! :-)