They usually mean the same thing, but it depends on the school. I am on alternate lists at UVM and UF, but I know that they are both waitlists.
Actually, I bet you are taklking about UVM, b/c I got the letter today and it says "qualified/alternate" list. Read my reply to thundercat in the Allopathic forum for an explanation of how their waitlist works (in case you're wondering).
~Michelle