Well I just purchased a book and used the code. The price changed and I pressed the "Buy Now" button but on the next screen I got a message telling me that I had been charged the full price.
A quick call to my credit card provider and they say I have been charged the reduced price!
So it seems like a bit of a bug with the original price coming up on the second page instead of the discount price. Hopefully the others who thought they had been overcharged have really got the deal they thought they were getting.
I have asked Kobo what is going on so maybe they will get back to me.