This same exact thing happened to me recently...
I booked a B fare and ticketed it, but then after I rec'd a confirmation e-mail, I got another e-mail saying there was a ticketing delay. After 1st call to CO web support, I check my itnerary online, and it showed all S class!
I called back, and they were able to see where the website had shown me the inproper class, but said that they would honor what the web said, and re-booked me in B at the same price.
Just keep after 'em and they should book you in the class that the web showed...
K