There are some automatic handling processes in place for comments and it sounds like you've run into one of them.
If a comment contains a black-listed word, then a single flag will remove it.
The second auto-handling is based on the number of flags on a comment. Once a comment reaches a specific threshold, it automatically deletes the comment and the flag is processed as helpful. It's entirely possible your flag pushed this comment over the edge so it self-destructed. See this Meta Post for more details:
Comments that are flagged by multiple users are deleted automatically. The number of flags needed is based on the comment's score. It currently takes "3 + (Score / 3)" flags to delete a comment.
It has nothing to do with the type of comment flag, it is based on the number of flags a comment has on it.