I would email them to double check if you haven't already. I can't find it now unfortunately, but while neurotically trolling another school's thread from last year for something else, I saw a comment that the school sent everyone they admitted a Certiphi link and a lot of people did it twice, but it turned out it was only meant for people who had not done it yet.
However, in that case, I didn't see any mention of it being $55. It's weird they would send you a non-free one for MD admisisons. Did you apply to a dual degree (MPH/PHD/etc?).