Could be the last blurry photo talking, but are you sure that's pox and not just embedded grains of substrate? Many palythoa will incorporate it into their polyps. And you know how big wholesalers are on proper identification before they distribute something, right? ;-)
By all means continue with the treatment regimen since you're already through day 1 of three... done correctly it won't have any bad effect on a healthy colony and if it IS pox could have a good chance of knocking it out. It's not like you're going to lose either way.