What is your PATH environment variable set to? Are you sure you do not have Java 1.3 installed somewhere?
Do you have Oracle database client software installed? Older versions of the Oracle client software installed a Java 1.3 JDK along. Make sure the bin directory of your Java 6 JDK is in the PATH before any other Java installations on your system.
Rob: In my experience that doesn't always work correctly, in some versions of Windows (?) it might set PATH before it sets JAVA_HOME, and then you'd have a literal "%JAVA_HOME%" in your path instead of the real path.