Once again, it’s happened. The new release of MC, 1.4.6, is not backwards-compatible with 1.4.5. The server is still running 1.4.5. So, if you want to continue to play on this server, either do not upgrade, or be prepared to downgrade.
As usual, we are waiting on a stable build of Bukkit for 1.4.6 before we can upgrade the server.