I remembered getting a Java update within the last week, too. Only one, though, not two. So I ran my normal AV Scan (Norton), and just finished running Malwarebytes and Spybot scans as well, and no viruses.
I'm wondering how you determined that the problems came in with the Java updates? I know the site has been having problems and they seem to have been fixed, coincidentally, at about the same time you're problem was solved. And I've never had a problem with official updates from reputable companies, except Microsoft. And those are usually just bad updates, not viruses.
I'm also curious about whether you allow the updates to install automatically. I'm a suspicious cuss, so I have things set to inform me when updates are available, then I do a manual install. The only thing I have updating automatically is my AV.
Anyway, I'm glad you got it straightened out. I know from experience what a royal pain in the neck it is to have to deal with that crap.