Installed the server as download offered at
https://mojang.com/2013/06/minecraft-1-6-pre-release/
Tested on a Windows and a Linux PC. Each time the server claims to be version 1.6.1 however when trying to connect with a client, it says it's 1.3 and won't let connect anyone.
Duplicate of MC-19592, please use the search function to see if your bug has already been submitted. Currently over 57% of tickets are being closed as duplicate.