I'm having the same problem here in Brazil. I'm calling Mexico DF and the rate in the site is 22 cents per minute, when I make a call, it's charging me 77 cents per minute.
I don't get it as well.
I've been trying to find an e-mail to get in contact with Skype but I can't find any.
I guess I will have to cancel this account and start using another software, since my father who lives in Mexico and I in Brazil both have the Iphone 4, we will start using VIBER.
If you can find out what's going on, let me know.