1) if banning his IP doesn't work, then he probably has access to other computers with MineCraft on them.
2) WhiteListing would work, until other players got annoyed that they couldn't join your server... :/
3) IF this was in the 1.6.2 version, then it could be because of a glitch in the system. That's why the 1.6.4 version came out so fast. the glitch aloud players to hack into servers, and into the concole that the server is on. try a FULL computer scan of your virus protection.