You may be running afoul of Vista's compatability shims.  Certain keys
and certain filesystem paths are redirected to per-user versions of
themselves when accessed by apps running as a non-admin user.  This is
intended to minimize the number of crashes under non-administrator
accounts for apps that assume they have admin privs, such as yours.

jRegistryKey is writing to the key you're requesting, but Windows is
redirecting that write.  In order to have an application run at
startup, you must make the appropriate changes *as an Administrator*.
Any other registry manipulation library for Java would encounter the
same behaviour, as it's part of Windows now.

The right solution is probably to disable or remove that menu item
entirely unless the user is an administrator, or to dig through the
UAC docs on MSDN to find out how to escalate your privs for the
duration of the registry change.  The WRONG solution is to tell users
they have to run as an admin; that's the sort of thing the entire
internet has been trying to get Windows users away from because it's
so bloody hazardous.

Details here: <http://msdn2.microsoft.com/en-us/library/bb530198.aspx>

On Sun, 04 Nov 2007 12:11:13 -0800, JediKnight2
<JediKnight2@gmail.com> wrote, quoted or indirectly quoted someone who
said :

A lot of vista problems have to do with permissions.  Try the
run-as-administrator option when you run you app.  Right click the
properties on the launch icon to set it.

If that does not work, check with the  jRegistryKey authors to see if
they know what is going on.  

If that does not work, write traditional C++ code to poke the
registry, and look up to it with JNI.

Hold your nose. The code required is disgustingly verbose.