Not sure this will affect anything but try deleting (renaming, moving, whatever) the following file in your account:
where the X's are a sequence of hyphanated letters and numbers.
Also might try another account. And also see if booting in safe mode has any effect.
It's just a preference file (preferences usually are .plist files). If you don't want to delete it just move it to your desktop. A new one should be created. The idea is that maybe (just maybe) it's corrupted in some way so let a fresh one get recreated when you run Java Preferences.
Using another account would similarly using the one in that account or create one when needed, say if yo9u launch Java Preferencs.
Booting in safe mode suppreses all third party start items just to see if it is something you added to your system that is confliting with java.
I too have the same Java problems.
Java apps do not run within any browser; Safari, Firefox or Chrome & stand-alone Java apps do not run.
I've tried deleting various "plist" files, etc. etc. I've tried installing/re-installing Java from Apple's site, but it says I already have a newer version installed.
According to the tests, I am not infected with the latest virus.
My son wants to play Minecraft, so I had to send him to a PC...sad, very sad.