I've heard that if your uvs are messed up, it can cause this. As I said earlier, I deleted faces on the low poly model that you can't see, and then fixed them on the equally tesselated model that i imported into zbrush. The uvs for these faces are unsewn and may be overlapping, but I don't see how this would affect other parts of the model, or the texture in general, as I didn't even use zmapper on those specific uvs, and they were in their own subtool group.
If anyone could help solve this problem of mine, I would be most grateful.
Thanks in advance.
PIC1: the low poly model in maya
PIC2: the high poly model in zbrush.
PIC3: a closeup of the resulting normal map on the low poly model.
PIC4: The actual normal map.