@tridacna - I interpreted his original post as saying that he was swimming the fins to get used to them in general, and if they worked out any different muscles to get that conditioning under way. Which he described as "breaking them in." And in the process of doing that, he discovered this other issue. Better to discover that now than on a trip!!
I did not interpret his post as saying that he found some discomfort and so decided to keep plugging away in the hope that the equipment or his feet would break in. So, @KenLovely , your original question was perfectly reasonable and understandable. Sorry we couldn't be more help. (I'm still wondering what size fins you are breaking in, and if that is the issue.)
@JackD342 I read it differently. "The top of my foot hurts like mad. The area shown in the image". Image clearly indicates where the fin-pocket meets the instep. That is not from muscular discomfort due to unusual activity. That's from a pocket that does not fit properly. Calf pain or cramping is a typical response to a new fin or activity.