Avast found Win32:Malware-gen, Win64-Sirefef-A, and Win32-Atraps-PF

I seem to be having problems with Java. I ran JavaRa and it appears to have deleted all Java versions. I went back to the Java site and reinstalled the latest version. The installation process appears to conclude successfully, but the Java version checker doesn't recognize any version of Java installed. I ran JavaRa again to try and start from scratch, but the exact same thing happened - installation appears to be successful but the Java site does not recognize any version of Java as being installed. Java applets are showing up as empty boxes wtih a small red X in the upper left corner.

When it did it the first time, the Java site did recognize an older version of Java and recommended an update, which I did.

Have you experienced this before? Any ideas how I can get Java back up and running? I'll continue working the issue on my end, but the last two hours have not yielded any results so I'm officially asking for help.

I'm trying to uninstall Java and start from a clean slate. Following the uninstall directions from the Java site indicates that uninstallation should take place from the "Add/Remove Programs" section of Control Panel. In the list, the previous version of Java (Java 6 Update 29) was listed as still having been installed. I tried uninstalling it, but the uninstallation process returned a fatal error.

The program list also shows the latest version of Java (Java 7 Update 5), so I tried uninstalling that also. Unfortunately, that process also returns a fatal error.

I also tried running JavaRa to uninstall old versions again to see if that would help. The JavaRa log file shows that it isn't finding any old versions of Java.