I was doing some testing on a server with a friend of mine. We found that:

• You can move bedrock with the builder. I don't know if this was intended.
• You can move the End Crystals that heal the Ender Dragon. Not really an issue I suppose but I don't know if it's intended.
• You CANNOT move the End Portal inside of The End. If you try, it will crash the server. It moves the bedrock blocks but I believe in it's attempt to move the portal blocks it causes the crash.

I need to protect this. Thanks for reminding me :-)

Fixed in next release