@eireen Hi, you are not doing anything wrong.
Apply Location moves the Origin of an Object to Location (0, 0, 0), the World Origin.
But an Empty Is actually only an Origin.(Yes an Origin also has a Scale and Rotation!)
So, if you move the Origin of an Empty (for instance by Applying the Location) you move the whole Empty. (I hope that makes sense…)
I do not know how the Empty was messing up the Array in your case (it’s really powerful, but can be tricky to get it right if you’re not used to it…), but, like I said, Applying Location with an Empty is the same as Clearing its Location i.e. putting it at the World Origin (0, 0, 0).
If you give more information I ( or anyone else here at CGCookie) will be able to help you for sure;)
