Odd pixels when AO Baking

Hey, so I’m not really new to texturing and materials but this is really confusing. Whenever I try to AO bake to this UV map, I get incomplete bakes and pixels. This does not happen with the main object (Hierarchy to the right side of the picture) but with all parented objects this is a problem. The UV map was made in Texture Atlas.
Any help would be appreciated.

If this is in the wrong forum please feel free to move it.

try in edit mode:
W -> Remove doubles

I’ve already tried that. I have also reset all normals and made them consistent. Anything else I could do?

Anything else I could do?
Attach or post a link to your blend file. Then we don’t have to use guesswork

Okay. Here is a mediafire link. http://www.mediafire.com/download/972k4kyd40hklpi/Nuadha01.blend

Here ya go. http://www.pasteall.org/blend/24854

You have a mirror modifier on this object which is of no use. All it is doing is duplicating your whole object to give in effect overlapping faces. Remove the modifier

Thanks, I completely forgot to remove them after I separated them. Facepalming hard right now.