That's just how it is, the link command does not show all know backlinks, only the ones taken into consideration.
Have you noticed the new tool in the Google sitemaps account ?
There is a new link menu where Google tels you more about the links he knows about.
And obviously, the difference in results you point out comes from the difference in the search query.
You're just not asking the same thing and get different answers.
Searching for www.phpbb-seo.com
only will include inactive links such as -www.phpbb-seo.com, as part of the content's text.