I know that sounds rather simple, but if you read the privileges page, you will find out that:
The offensive and spam flags are designed to automatically eliminate truly offensive posts through the collaboration of the community.
3 flags -- post is banished from the front page. 6 flags -- post is locked, deleted, and the owner loses 100 reputation.
Users with the Moderator Tools privilege can see how many offensive flags a post has accrued, and may opt to flag it themselves.
So, my question is, if it has been already banished from the front page, how is it possible to flag it again? Wouldn't it mean that the actual maximum is three, not six?