Hey, I'm suffering this issue too! The game didn't seem to scan my codex entries either, so I'm missing a ton of achievements I should have gotten. I'm going to try to send tickets in-game until it gets resolved.
This is a quote from the official blog post
from the achievement introduction:
On day one, we will automatically grant Achievements for everything that can be easily verified and tracked on your character. Any quests you have completed, codices you have found, items you have, pets or vehicles you have collected, or levels you have attained will all be counted towards immediately updating your Achievement progress. You will likely find that you have many Achievements already when you log in to Game Update 2.0 for the first time.