Install JDK in D:\Apps\1.3.1, but classpath=C:\Program Files\JavaSoft\JRE\

I installed the 1.3.1_01 JDK at D:\Apps\1.3.1, but a second copy of the hotspot jvm is installed at C:\Program Files\JavaSoft\JRE\1.3.1\bin. I can find no way to prevent the JDK install program from doing this (w2K sp2).
I wouldn't care, but many programs keep using the C: version. My PATH variable only points to the D: directory, but if I open a cmd window and type java it runs the C: copy. When I installed JEdit 3.2.2 it starts up saying java.home is C:\Program... and I should add tools.jar to my classpath. Well, tools.jar is in my CLASSPATH. It points to the tools.jar on my D: drive!
Does anyone know what is going on? How can I get all programs to point to the java.exe version that is specified in my environment variables?
Thank you in advance,
Kevin

Under Windows, some programs assume that Java is started by %Windows_Dir%\System32\Java.exe. This version will look in the registry to get the current version of Java. The key it checks:
HKEY_LOCAL_MACHINE\Software\Javasoft\Java Runtime Environment\CurrentVersion
In my case, this key says 1.4, so it goes into the 1.4 registry key and finds this:
JavaHome=C:\Program Files\JavaSoft\JRE\1.4
So that's where it generally comes from.
If you explicitly run the java.exe from a specific Java install directory, it will use that directory as the home though.

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