http://www.seoprofiler.com/company/about compares to Google link: queries, which are indeed incomplete. How does your crawl compare to Yahoo! Site Explorer link: queries. The latter seem more complete to me.
SEOprofiler shows the backlinks only for the creativecommons.org subdomain, excluding support.creativecommons.org, wiki.creativecommons.org, search.creativecommons.org, de.creativecommons.org, etc. For this reason, the backlink number appears to be lower.