It looks like your company is paying for these links, Google-and other search engines- is pretty good at determining paid links from natural link (run of site links like this are usually a give away). Google drastically reduces the value of these links. While the sites may call it a sponsorship with the benefit of having a link, Google sees that as you are basically buying links, meaning these people wouldn't normally link to site; therefore these links are not a true sign of importance for your site. I would focus on building 'natural' backlinks from other sites.
To address your question of why Google is not showing the same amount of backlinks for the two sites, the most probably answer, is that Google really isn't a very good tool for determining backlinks. They only show a sample of backlinks for a site as not to give competitors backlink information. Use Yahoo with the site command to get more accurate backlink info (although the do contain nofollowed links)
While the number of links are important, it is not as important as it used to be. The number of links used to be very important, but this was easily manipulated with run of site links and footers....Currently, the number of pages linking to a site are important, the number of domains linking to a site is considered by some to be more important. Focus on building links from different domains rather than just lots of links from a few domains.
