Pivot Point Problem

Hey, so i'm having a problem with the pivot of an object. A couple of my models when put in my torque mission come out faceing the wrong direction and then I have to rotate it and such which isn't that big of a deal. However, I figured adjusting the pivot points would only take a minute and make it more convenient. So I was adjusting the pivots with the effect pivot only tool Hierarchy tab/pivot, and came across something odd and it's the first time i'v seen this. When adjusting the pivot only on a model which contains 2 pieces, the top part works fine when adjusting. But when I try and adjust the pivot only on the bottom piece (which is only a box) it adjusts the whole object rotating it when I only want to rotate the pivot point. Anyone know why it's doing this?