What is installed with Java 7?
The Java Control panel in System Preferences refers to the Java Applet Plugin (JRE) that is made available to Safari and other browsers.

If you use the Help>Installed Plugins you should see a version signature if it is enabled The latest JRE reports

application/x-java-applet;jpi-version=1.7.0_13  


The java you are looking at with java -version is the one installed with the full JDK. You  need to download the installer for that separately now from Oracle
When installed java -version should report

java version "1.7.0_13"
Java(TM) SE Runtime Environment (build 1.7.0_13-b20)
Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode)