Yes, they are different. The first sentence is certainly a greeting. I haven't heard "How are you going ?' as a greeting . Maybe " How are you going there?

Of course, I might be wrong, but as I know, there's no such expression as "How are you going". Probably, you confused it with "How IS IT going?", which means the same as "How are you doing?", "How do you do?" or "How are you?"