Hey Chris,
From your description, the first thing that springs to my mind, is that you have inconsistent Normals; in Edit Mode, Select all (with A) and then SHIFT+N.
Inconsistent Normals happen all the time, when modeling and are not a mistake on your part, simply something to be aware of. If you get any strange results, this is one of the first things to check (just after double Vertices and a Scale that is not Applied.)