I can't tell much from that picture, even though the second one is very clear. I still can't tell if that is something on the cork that is discoloring it, or if a chunk of cork is missing. Anyway, it doesn't look good.
I keep my floor corker covered with a plastic bag when not in use to keep dust off it. I spray all the surfaces of the corker that touch cork or bottle with Star San before corking. I fumigate my corks in a cork safe (a collander inside of a closed bucket suspended over a bit of sodium metabisulfite) for a couple of hours before I cork. Haven't had a problem yet.
If you cleaned and sanitized the corker, I'd suspect the cork was bad to start with rather than the corker.