When /clone, /fill, and /setblock are used for setting blocks outside the world border, they cannot set the blocks.
To recreate:
1. /worldborder center ~ ~
2. Move away from center
3. /worldborder set 1
4. /setblock ~ ~ ~ dirt or /fill ~ ~ ~ ~ ~1 ~ dirt or /clone ~ ~ ~ ~ ~1 ~ ~1 ~1 ~1
Intended.
Also, your Java version is OUT OF DATE! Please update to the latest version, which can be found here: http://www.oracle.com/technetwork/java/javase/downloads/index-jsp-138363.html