Mako might be a "Guest" companion at that point. IE, she isn't a real companion yet and can't earn affection points. The other posters are correct as well. The affection gains you see in conversation actually appear on her character sheet when you turn a quest in.

When I started playing WoW, I thought it was awesome that we could use addons. It was great, I could feed my pet without actually doing anything. DPS meters allowed me to see what was the best rotation. Heals, etc. CC, who broke what. After a while you couldn't play WoW without those addons. Look at any guild that runs raids; do they have a list of required addons? The Old Republic is a new game. Relearn how to play without relying on addons.