I've ordered from them and only had minor problems.
At this point I would not be sending back the box you got that was duplicate.
I would send them an email that you want a customer service rep to call you and discuss your individual issues.
Once you get a satisfactory response then you can either send back the box or get the items you want to keep paid for and return the rest, or just pay for it all! There is NO reason that they cannot correct your order and get it squared away!
You've done everything right. You notified them of their error. Now it's their turn to fix it in a way that works for you!