Hi sidosquiere,
Carafate was developed to help protect healing stomach ulcers from acid. I was told by my doctor that it is a very benign drug, and that most is excreted, and very little is absorbed. I have used it for years, since I have a very reactive stomach, and I find it extremely helpful in getting things feeling better.
I do not think the Carafate is the problem, unless for some reason you're reacting to it in some sort of allergic way. Did you call your doctor and ask this question? I'm a big advocate of Carafate suspension just because it coats and protects the esophagus. I can't imagine that it is causing your problem.
Here is a link to a list of possible Carafate side effects:
http://www.rxlist.com/carafate-suspension-drug/patient-images-side-effects.htm
Please call your doctor and report your concerns. I'm confident that it isn't the Carafate, but your doctor should make that determination in any case. Your doc should know the troubling symptoms you're experiencing.
Good luck! Hope you get things healed and cleared up very soon!
Best wishes,
Denise