You can flag comments as often as you like, if the flags are dismissed in the meantime (as far as I understand the rules). Comment flags are not attributed to a specific user, which leaves open a way to abuse these flags. You can repeatedly flag the same comment until you reach a moderator who finally deletes it. While comments are expendable, this kind of repeated flagging wastes moderator time and gives users who are willing to bend the rules to their advantage a better chance to get comments deleted they dislike.
Either repeated flagging of comments should be disabled, or the moderators should get some indication that the flag is a repeat. Moderators currently can not distinguish if a comment was flagged three times by different users (while the flag was dismissed in the meantime), or three times by the same user. And I think there is a significant difference between these two cases.