Ok, I have finally managed to cleanup the old config paths - these were in the registry at various locations, such as:

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Installer\Folders
HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Java Development Kit\1.6.0_31
...

What you need to do is search in all keys/values/data for the JDK signature, e.g., "1.6.0_31", also search the wrong JDK paths, e.g., "hudson" in this case.
Then all remote installations from the master of JDKs will proceed in the proper places.

I guess the headless installer that forces 'yes' on all questions, also uses any default suggestions that the installer may make for directories, and an existing one happens to override the instructed place to install <argh>!

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