For ages, I've wondered how in most cases, java will mysteriously be in your path in windows, even though there is no Java install directory in the path. (it will certainly be a version that was installed with a proper installer, at some prior point, but not necessarily the most recent version you've installed) To fix this, I generally put %JAVA_HOME%\bin; at the front of my PATH environment variable after defining JAVA_HOME to point to the Java install I care about (something Ant, Maven, and other dev tools often care about having defined...).
I've always wished I had the 'which' command in Windows, so I could locate which Java executable was in the path. Finally, by chance, a coworker was debugging an OpenGL crash with an Intel GMA graphics card and substituting DLLs in what he thought was the 'run' directory, and he realized that it wasn't picking it up when he put it in the directory of the JDK bin he thought it was using... When he checked process explorer, lo and behold... C:\WINDOWS\SYSTEM32\java.exe is what was running. What the heck??? I find this strange, yet there it is.
I have always thought it was registry magic, or some other trick that caused Java to end up in the system path unless you put it as the FIRST path entry. Instead, FIRST just means AHEAD of the System32 folder. (Several apps likely to be in a dev environment often put themselves at the front of the path, subversion, oracle, etc...so I never noticed that the usual first entry in the PATH is this...and I typically put entries at the END of the path except when I know there will be other entries fighting for this position)
It's funny how sometimes mysteries like this go on for many years - maybe it's a simple Eclipse feature nobody knows about, or some maven quirk, that we never take the time to fully investigate and understand...we just come up with the rule and follow it - at least it's what I've observed.
If anyone can shed some light on this, I'd love to hear it. Is this practice generally acceptable to pollute the SYSTEM32 folder with executables? For now, I am satisfied to now know why I need to put my java/bin at the front of my path...