Issue with Java applet

Question

I am having issues with an "inactive plug-in" message in Safari when I want to do something using a Java plug-in.  I searched the communities and sure enough, when I opened Java preferences the box next to "enable applet plug-in and Web Start applications" the box was unchecked so I checked it.   Unfortunately, when I go back into preferences, the box is once again unchecked.  I did find out that I had a Trojan in the user.jar file associated with java but despite taking care of that issue (which for all I know is not related), this issue persists.  All of my software is up to date and from what I gather uninstalling and reinstalling Java is not an option and should not need to be fone.  I'd very much appreciate any input!

Answer 1

Repairing the permissions of a home folder in Lion is a complicated procedure. I don’t know of a simpler one that always works.
Back up all data now. Before proceeding, you must be sure you can restore your system to its present state
Launch the Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the page that opens.
Drag or copy — do not type — the following line into the Terminal window, then press return:
chmod -R -N ~
The command will take a noticeable amount of time to run. When a new line ending in a dollar sign ($) appears below what you entered, it’s done. You may see a few error messages about an “invalid argument” while the command is running. You can ignore those. If you get an error message with the words “Permission denied,” enter this:
sudo !!
You'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning not to screw up.
Next, boot from your recovery partition by holding down the key combination command-R at startup. Release the keys when you see a gray screen with a spinning dial.
When the recovery desktop appears, select Utilities ▹ Terminal from the menu bar.
In the Terminal window, enter “resetpassword” (without the quotes) and press return. A Reset Password window opens. You’re not going to reset the password.
Select your boot volume if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select  ▹ Restart from the menu bar.