If you use a registry cleaner, you’re most likely going to have to run runonce.bat to restore the Softimage registry entries. For example, see here and here.
A recent thread on xsibase touched upon whether or not registry cleaners are necessary. Personally, I doubt it. I recently googled “registry cleaners” and went through the first 20 pages of results. Most of the hits were sites selling registry cleaners, and most of the URLs had “registry cleaner” in them. In those 20 pages of google hits, I found only a handful of pages that had a substantive dicussion of registry cleaners, and I didn’t find any performance metrics or results.