I'm not sure about elsewhere, but at Emory, the difference was that the BS required a few extra classes, or taking a higher level of a particular class. For example, there were two different levels of physical chemistry - a more advanced version required more calculus. I believe the more advanced one was required for the BS but not the BA.

I don't now if certain jobs are more likely to consider someone with a BS over a BA, but it didn't seem to matter much for getting into medical school. It also might be better to have the BS if you are going to graduate school in chemistry. I would guess that most people going to graduate school in chemistry would already take enough courses as an undergrad to qualify for the BS anyway.