If the sites are related in theme, have some content and some pagerank, chances are very good that you are getting some kind of credit.
Your SEO guy is wrong, you can’t micro analyse your link partners like that. The best you can do is evaluate the quality of the site and page that is linking to you and make an educated guess about the value of the link. You can check cache:http://www.pagethatyoursiteislinkedfrom.com/links.html on google to get a sense of how frequently it is spidered.
Google wants to give you an idea about who is linking to you, but they don’t want you to be able reverse engineer their ranking algorithms so they don’t show all incoming links.
Also, there are no bad links, just make sure that the anchor text is keyword relevant.