If run Java on a Vista system with enabled UAC (User access control) then the preferences of the
system root
are only visible to one user like the user preferences.

The cause is that Vista link the registristry to
HKEY_CURRENT_USER\Software\Classes\VirtualStore\MACHINE\SOFTWARE\.....
if the user has not the required rights. This behaviar is bad. It should throw a SecurityException.
Or it should
return the preferences only with read only like on Linux.
 
We use the Preferences to setup the configuration for programs on other user accounts and services
on the system
account. A workaround is to run the program with administrative rights. But we does
not can detect it. That we
cannot inform the user about the problem.

The Java runtime can check if a write operation produce a key in
HKEY_CURRENT_USER\Software\Classes\VirtualStore\MACHINE\SOFTWARE\.....
Then the system preferences should be read only.

This problem occur with all Java versions. Also with 1.6.0_02b3.