Ok well I just got my server working to day (permissions) and 1h after i do my friend can't join because his launcher says that the server is outdate. He can't join. My server is 3.1.3 . PLEASE HELP!
3.1.3?! I think you mean 1.3.1 right? If so, that would explain pretty much... Your friend's client is alread on 1.4.6 that means he cant play on your "outdated" server. Update your CraftBukkit or bring him to downgrade.