I've noticed this behavior for a while, but was just asked about this by a co-worker. The Google link: operator does not really work as most people expect and certainly not the way I originally expected it to work. Google has this to say about the link: operator:
The query [link:] will list webpages that have links to the specified webpage. For instance, [link:www.google.com] will list webpages that have links pointing to the Google homepage. Note there can be no space between the "link:" and the web page url.
Notice they don't explicitly say anything about the accuracy or volume that will be returned, just that it will return pages that have links. Well, that's not even really true. Sometimes it will return empty results (even when there are legitimate external links to a page (could be even thousands of links.)
If you're really trying to find external links to your site, the best method Google provides is via their Google Webmaster Tools (see How can I see links to my site?.) Even this method apparently won't reveal all external links, but it's much more accurate.
If you have any great tips for listing external links, make sure to share them in the comments.