Maybe I'm misunderstanding.
Well what I did was, added the word amazon to the list of words, and set the URL to
http://www.amazon.com
Then I did a search for threads with the word Amazon in it. I checked one out, a thread from a while back, has the word amazon in the first post. The word is definitely getting hyperlinked via your mod, however that link is not getting "skimlinked". So as of now I don't think ANY links created via your MOD are being changed by skimlinks.