Vista introduced registry virtualization; "global" registry changes are, in some cases, redirected to user-specific locations:
Registry virtualization is an
application compatibility technology
that enables registry write operations
that have global impact to be
redirected to per-user locations. This
redirection is transparent to
applications reading from or writing
to the registry. It is supported
starting with Windows Vista.
This form of virtualization is an
interim application compatibility
technology; Microsoft intends to
remove it from future versions of the
Windows operating system as more
applications are made compatible with
Windows Vista. Therefore, it is
important that your application does
not become dependent on the behavior
of registry virtualization in the
system.
You can disable this by customizing your application manifest, or you can modify policy for just the key you're touching.
WOW64 (are you running a 64-bit edition of Vista?) also does registry redirection. This has bitten me in annoying ways.
See the MSDN article on registry virtualization.