Maybe most of the popular search engines are mostly counting links from high Authority websites like Huffington Posts, Gawker, Game Spot, GameFaq, GameSpy and other highly successful sites, and care less about backlinks from sites where anyone can post a link, or easily buy a link like forums, blogs, personal sites, and social bookmarking sites.
The only way to know is to contact a search engine employee, but they usually keep their rankings a secret.
I think Google hides some of your backlinks, or it takes time for them to show up in Google Webmaster tools, or Google search according to a video I watched on Google's YouTube channel for Webmasters.
It does take quite a while for them to show in Webmaster Tools. If you're interested in a bit better backlink reporting, I suggest Majestic SEO. Also know that forum profile links have lost a lot of importance when linking directly to your site. They're better for using in a pyramid and pointing them at a buffer site.
What's more probable? That Majestic randomly "made up" URLs that are pointing to your site, or your other tools aren't detecting links you actually have?