Tracking achievements

I'm unable to find any reports of a known issue like this at the moment, Mordecai, but I have seen a couple reports of this happening. Have you tried resetting your User Interface? Can you try the steps below?

Q u o t e:

1) *IMPORTANT* Exit the World of Warcraft to your desktop by logging out of the game and exiting. If World of Warcraft isn't closed, then these steps won't have the desired effect.
2) If you used an "installer" for a custom UI, see if it has an "uninstaller" and use it.
3) Inside the World of Warcraft Program Folder, delete the "WTF," "Cache," and "Interface" folders.
4) Restart your computer.
5) Please do not reinstall Addons prior to testing the issue you were experiencing.
6) Make sure that you are using WOW.EXE or LAUNCHER.EXE to start the game. Please do not run any UI installers beforehand, as we want to eliminate them as part of the issue.
7) Upon launching the game, you should see the Intro cinematic movie and be prompted to agree to the Terms of Use. Once you authenticate past the login screen, the “AddOns” button should no longer be visible at the lower left corner of the character selection screen. Both points mentioned previously must hold true if you should complete the aforementioned steps correctly.

If you continue to experience this issue please post as much information as you can in our Bug Report Forums so our Quality Assurance Team can take a look at it.

Q u o t e:
I believe I found the cause of this issue. Tracking quests and achievements are shared so when I had two quests being tracked, it wouldn't allow me to track any achievements.

Ah very possible. The only issue I have seen with this is that sometimes when you are tracking a quest and achievement the information can overlap on your screen.