Hello zpm2014,
This is the most common question that I have seen. People are asking in forums why the disavow tool isn't working for them, so here is the answer to your query.
When a link is disavowed, the next time that Google crawls that link they essentially add an invisible nofollow tag to the link. There is no external evidence of this. Just as your nofollowed links are listed in WMT, so are your disavowed links.
In this webmaster central hangout Google's John Mueller said, "Disavowed links stay in Webmaster Tools" and in this hangout he said, "When you disavow links we will still show them as inbound links in Webmaster Tools."
I hope that your query has been solved.
Regards
