A sanity check on the registry operations is that on typical systems they should take significant time - registry tends to be big. If they aren't taking significant time (a few seconds at least I'd guess), then I suspect you need to manually make a deep copy of the registry structure and compare copies.

Another non-Perl option that may be worth considering is InstallWatch which will catch more than just registry changes, but can take a while to run and need a fair chunk of disk space.