In my version of IE (version 9) there is no mention of Java in the Advanced tab.
If you have just reloaded to factory settings, make sure that you have all your drivers installed first (Chipset Drivers should be the first to be installed and the order of the other doesn't matter)
Then do all your Windows Updates (Service Pack 2 is the latest one for Vista)
Update your Java
What anti-virus are you going to choose? I'd recommend Microsoft Security Essentials
, but beware that as your computer has been restored back to factory setting, you will probably have some bundled software on there that you may want to uninstall? I'm guessing that it may have come with a trial version of McAfee or Norton.
It's completely up to you should you wish to carry on using them, but should you want any help cleaning out unwanted bundled software, just let us know.
Once your computer is completely up to date (drivers, Java updates, IE9 etc) post back.