I don't understand the $11 part.
Do you think he meant to say that they'll refund you the $19.95 for the boot but will not refund the shipping costs?
I know you said you paid $12 for the shipping, so maybe his email had a typo.
That is really crappy though.
I'd call Andy's back and try to talk to someone else and resolve it that way. If they absolutely refuse, then do the claim with your credit card company.
People on NECO have had problems with Andy's in the past.
