Did you completely un-install the old version first and then clean your system with a tool like the free program "CCleaner" to ensure all of the old registry keys and program file folders were gotten rid of prior to installing the latest version? Java is another program (like Adobe Flash) that if you simply install the latest version over it, you still will have issues with vulnerable components being installed.
Locations like:
C:\Documents and Settings\"profile's name"\Application Data (Make sure the Sun folder no longer exists under any profile you may have on your system)
C:\Program Files\ (Make sure the Java folder no longer exists)
C:\WINDOWS (Make sure the java folder no longer exists)
C:\WINDOWS (Make sure the Sun folder no longer exists)
Make sure the files: java.exe, javacpl.cpl, javaw.exe, and javaws.exe no longer exist under the C:\WINDOWS\system32 folder.
Can you post your Retina scan result into this post too that is telling you that your Java is not correct?
You can also look at this post also, another user was having similar issues: http://forums.eeye.com/forums/p/960/4135.aspx#4135