Jarrod Dixon, a developer for Stack Exchange, said [in a comment](https://meta.stackexchange.com/questions/185866/flag-count-is-missing-from-profile-pages/185889#comment570008_185889) that comment flags weren't being counted correctly before; so in the new build your flag count *includes* comment flags (if that makes any sense..)

Comment flags now appear in your flag history as well.