I checked with my friend who made the server with the invalid server key issues. He was using the download right off the main site and the issue was still there. He had to look up the fix and he found out that it is the Minecraft_Server.exe that causes all the server key problems and the Minecraft_Server.jar version doesn't have the invalid server key errors.
Don't use the packaged .exe version that is downloaded off their website if you don't want server key issues with 1.01/1.0.0 servers.
They did officially patched, all those server hosts that make servers have to download the server software, ATM in the official website there is the official 1.0.1 server software which has the problem fixed, what are you complaining about?