Do you have a 'known good' backup from before you updated java? I would recommend (if you can) backing up all your personal files and rebuilding your OS. Then scan the personal file backup with an anti-virus and move over the personal files as you need them (ie, don't move all of them back on the new computer at once).
Finally, as I'm sure you've learned, only update an application through a trusted method (ie, Windows through Windows update, Java through the java icon on the toolbar, etc...), and be willing to close a browser and find a new page if a weird pop-up comes up.