I am tracking achievements - however, when I DO complete an achievement sometimes its 1/3 or 1/4 etc.. Why does ATT not register the achievements as finished? Ive gone through the settings numerous times and I would to be able to hide the achievements Ive collected and show the ones I still need..

Can you post screenshot examples of which ones you are referring to? That way we can see the behavior. Currently I haven't seen that problem and I've been tracking them since we implemented it. So seeing examples would help.

Here are two examples from Ulduar

For "Orbit-uary" it says you have the achievement, but you are missing "Boots of Fiery Resolution" so for that category you are 1/2 due to the missing item. The same goes for "I Love the Smell of Saronite in the Morning". It counts the achieve as collected, but you are missing the items themselves.

For Ulduar it's easier to have the HM achievement listed then the loot to help separate how to get that specific loot.