One of my users was having a problem using an online system that ran a java applet. It would just display a box with a red X where the java window was supposed to be.  I tried a few things before this to get it to work in case they are related to the fix.

1. Reset IE settings in Control Panel >> Internet Options >>  Advanced >> Restore Advanced Settings

2. Added the site in question to “trusted sites”

3. Went to Control panel >> Java >> Network Settings and choosing “direct connection”

What finally worked was  Control Panel >> Internet Options >> Programs and clicked on “Manage Add-ons”. Then under “Toolbars and Extensions” I had to enable the “Java 2 Plug-in 2 SSV Helper” by clicking on it and clicking the enable button. Then I had to close IE completely and open it back up and it came up fine. Hope this helps someone.