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.
You mean randomly throughout the world, or randomly around a specific area?