I replaced the 1.6.1 server jar in my server folder with the 1.6.2 jar and changed nothing else, now when I load up a world generated by that server jar in 1.6.2, it spawns players in random locations (not server spawn) unless they do /spawnpoint or sleep in a bed to set their spawns at a specific point. The server is running with JVM flags -Xmx2G -Xms1G and thats all.
EDIT: To clarify, this is what I've always done to update the server, just replacing the .jar and it has never to my knowledge done this.