to remember is that every manufacturer has their own take on "neutral" or "stability" or whatever configuration.
Some have wider or narrower toe boxes, harder or softer foam in different places.
If these shoes don't work for you, you need to return them and get another pair. If this shop doesn't work with and for you, you should (IMHO) vote with your dollars and find a store that will.
I'm surprised that they didn't have you run on a treadmill...people's foot strikes can vary a lot from walking to running. Do you still have your old shoes? What does that wear pattern look like?
The link below is regarding pronation
http://www.runnersworld.com/article/0,7120,s6-240-319-327-7727-0,00.html
This link covers over pronation.
http://www.runnersworld.com/article/0,7120,s6-240-319-327-425-0,00.html
This link covers supination, which is basically running on the outside of your feet.
http://www.runnersworld.com/article/0,7120,s6-240-319-326-435-0,00.html
Good luck.