There is a confirmed bug in Bukkit and some people think it also happens in Vanilla concerning the End Portal. When you transition back to the main world it has a tendency to put you in solid blocks and will suffocate you. Make sure to put everything into an Ender Chest just in case before transitioning back.
Bukkit is being way too buggy and too many people are losing extremely valuable items because of it. I switched us back to vanilla.
Bukkit released a beta for 1.6.2 so we are trying it out. While we are seeing if the beta is any good (so far seems unstable) we started running updates on our dynmap. Here are some new landmarks in case you want to go exploring.
Jordan’s tree and desert village
Another one of Nick’s bases.
Our new player Brent’s base.
And some random arrow pointing to nothing from Jared’s base.