Well something must've gone wrong, or there was an oversight. Hopefully it was of the unremarkable variety.

Again, is it a "trojan" or a "virus"? Get your terms together.

After I installed the earlier Java update, my MBP would no longer output a signal to my external monitor at home (mini DP to DVI), but it was outputting fine to my external monitor at work.

I just installed this second update and my external monitor at home immediately started working again.

In fact, the "Download" button brings down 2012-001, not 2012-002. The SHA1 hash of the "new" download matches that of 2012-001. At least, that was the case an hour or so ago when I downloaded it.

So it appears as if Apple merely changed the name of the entry on the Support Downloads page, but not the issue date or that to which it links (info or file).

As a person whose Mac was infected under Lion by this trojan, and removed it yesterday, I sure would like to know more about why Apple included another Java update 2 days after the first one.

Edit: Since posting, I have found what was changed by Apple in this new Java update. This is from Apple's Java mailing list:

Java developers,

Today we re-shipped our Java 1.6.0_31 for OS X Lion today to address a critical issue we found in Xcode and the Application Loader tool. This new "Java for OS X 2012-002" package is effectively identical to "Java for OS X 2012-001", with the exception of a few symlinks and version numbers.

For the sake of expediency, we have re-rolled the automatic update as our standard full combo updater, with the hope that most users have not yet been presented with 2012-001. We considered creating a delta update for users who already installed 001, but that would have made the process of getting these fixes to you take longer.

We apologize for the inconvenience, and would like to offer our thanks to the developers who caught this issue and reported it to us as quickly as they did. This issue only impacts Lion users, so Snow Leopard users have nothing to reinstall.

Over the next few days, we will catch up with producing updated release notes, tech notes, and developer packages with the revised 002 version numbers.

Manual download links:
Java for OS X 2012-002: <http://support.apple.com/kb/DL1515>
Java for Mac OS X 10.6 Update 7: <http://support.apple.com/kb/DL1516>

I'm wondering why I haven't received this Java security update or the first one in Apple's software update. Is the Java code this updates something that needs to be installed outside of a regular Lion install?

That link does not work for me. As I said, it downloads 2012-001. After installation, Software Update still wants to install 002.

Eventually, I captured 002 by copying the directory produced by Software Update (before the install completes and deletes it) - /Library/Updates/041-5436. I was then able to copy this directory to my other machines and install 002 by executing the package 041-5436.English.dist.

I understand that the Java packagers wanted to get a release out immediately and cut a lot of corners. However, I don't believe that they should have changed the name of the 001 update on the Support Downloads page.

If the update is only available through Software Update, they should just have pulled the 001 package from the Support Downloads page.

I'm sure that many people will be confused (as I was) by downloading what they believed to be the 002 update from the Support Downloads page, only to have it re-install the 001 package.

Since I found I was infected with this yesterday and removed it, I was told to download the "Little Snitch" app, which I googled and installed the 3 hour demo of. I thought my system was clean of this trojan, as I followed the F-Secure removal instructions, but it appears this trojan installs other stuff once it gets in (via the Java exploit).

Little Snitch informed me that a file named .rserv (~/.rserv) in my Users directory on my Mac was trying to connect to cuojshtbohtnet.com or .net and several other strange sounding web sites. I denied them doing so and Googled .rserv and another program on my Mac that was doing similar attempts.

Also watch out for a file named: com.adobe.reader.plist in user launch agents directory. It was attempting to contact these same strange websites as .rserv was. I Googled these names and found in the last few days many other Mac users are seeing this same behavior when catching these "buggers" via the "Little Snitch" app.

Again, even though my system showed clean via the F-Secure instructions after I removed the infected files they mention, I believe I still had 2 other infected program files (same file date of March 29th also) related to this trojan that went undetected, and were only found by running this "Little Snitch" app which monitors programs trying to use your outgoing Internet connection.

I thought Apple got rid of Java, did I miss something?

Go to the Apple logo on the top and hit it and you will see Apple updates right there. I downloaded 2 today. i have the LION OS also.