I hate to be the one to say it, but the root of the problem is likely that you're trying to (having to...) learn differentials in a biochem class. There are so many other aspects of all of these diseases that it is artificial and difficult to learn them without a full grasp on those other factors.
What does a deficiency do to hematology? What is the GI involvement? Immunologic? Musculoskeletal? Reproductive? Any CNS effects? What are the histological changes? Gross anatomical? Is there a genetic cause for this illness? If so, what is the mechanism? Can it be acquired too? What clinical effects do those changes have? What are the common signs and symptoms? What are the current treatments? Side effects of those treatments? What other pathologies have similar presentations? Similar hematologic effects...
Learning a group of diseases in isolation, and only focusing on one or two aspects of them (say, hematologic effects, or genetic basis, or nutritional source) makes it very difficult to put the disease into the context of the complete picture. When you know everything a disease does, it is often a lot easier to differentiate it from another seemingly similar one (on the surface).
Maybe that's why I like the integrated curriculum, and why a lot of schools are going towards that model (and why the boards test that way...).