Here's how it works. If you played through the story before the trophy patch it won't read it an therefore you have to do it again or something a long those lines. During EA I mined atleast a couple thousand times an cooked a lot but when the trophy patch came out it didn't unlock them,I mined once an cooked something, an two trophies popped,so I had to redo everything again (same goes with monsters an fates).