I expect the situation is similar to the flu: once you contract a strain, you develop immunity to that specific strain, but as soon as the disease, which is under highly selective pressure to mutate, mutates, you are once again susceptible to the new strain. It might work for a short while, but not a full pregnancy.
There has been renewed interest in finding out what non-coding DNA (aka 'junk' DNA) actually does. Some prominent theories are that some kinds of non-coding DNA are epigenetic controls, but there isn't a complete set of theories yet. There ARE transposable elements, sequences of DNA that can essentially move around in your genome at will, and cause problems by doing so: imagine getting a transport protein sequence in a stem cell cut in half. Even then, these are kind of like DNA parasites, not junk.