Firefox – Need old version Firefox Java plugin

That's exactly where it belongs. From Wikipedia's WoW64 page:

The operating system uses the %SystemRoot%\system32 directory for its 64-bit library and executable files. This is done for backward compatibility reasons, as many legacy applications are hardcoded to use that path. When executing 32-bit applications, WoW64 transparently redirects 32-bit DLLs to %SystemRoot%\SysWOW64, which contains 32-bit libraries and executables. 32-bit applications are generally not aware that they are running on a 64-bit operating system. 32-bit applications can access %SystemRoot%\System32 through the pseudo directory %SystemRoot%\sysnative.

It seems that you have

• JDK 1.7.0_02 64 bit
• JRE 1.6.0_31 32 bit

JRE also puts a java.exe to c:\Windows\System32, that's how first command is resolved. Second command is resolved by the C:\Program Files\Java\jdk1.7.0_02\bin entry in your PATH variable.

If (and when) you are developing from the command prompt, you have to adjust the PATH variable so that C:\Program Files\Java\jdk1.7.0_02\bin is before c:\Windows\System32.

You can also persistently change the order, since Java browser extension does not depend on command line binaries and is installed separately.

My usual schema in windows is installing JDK's and also installing nested public JRE's whenever necessary. It's very similar yo your schema. You just need to adjust PATH variable a bit if you will be working from command prompt.