Hi there! I can definitely help clarify what's happening here.
I made Support copies of the following two mailings where links weren't being tracked: "Barrel_Tasting_2017_2nd_email" and "January_2017_Promo_0117". I see that you coded those mailings from scratch, and in looking at the code, I noticed image maps in both; however, we recommend against using image maps.
Image maps can cause problems in terms of HTML rendering issues, and they can break link tracking, which is what you're running into. Also, some mail clients (like Outlook) have a hard time accepting them -- so, you're best bet is to slice the image and link to its pieces. You can read more about image maps in this helpful Resource Center article.
That should clear things up, but give me a shout if there are any follow-up questions!