The Open Site Explorer indexed is completely refreshed every few weeks, and currently consists of 105 billion links. While that's quite a large data set and mostly comparable with other indexes in the space, it's still only a fraction of the links on the web and only a portion of the links Google undoubtedly knows about.
The way OSE finds links is that it prioritizes pages with lots of inbound links and links it found during previous crawls. Because BBB pages are often found deep-deep-deep under layers of navigation and usually don't have a lot of external links pointing to them, they aren't easy pages for crawlers to find on a regular basis. BBB has an especially difficult site architecture, and sadly this issue comes up a lot with that particular site 
We're working on including more historical data in the index, so that even if we didn't crawl the link in the past two weeks, we'll still include it if we are reasonably confident it still exist. This will help alleviate some of these concerns.
The good news (or bad depending on how you look at it) is that while OSE doesn't show every link, it tends to show the majority of the most valuable links.
Regardless, thanks for the feedback and best of luck with your SEO.
