Effect coordinates are relative to the layer and unless the layer matches the comp size, this won't work. You need to subtract the differences in width and height to compensate.
thanks for the reply Mylenium!
you mean i need to subract the difference in width and height between layer and comp from the effect? how do i do that?
diffX=thisComp.width-width; diffY=thisComp.height-height; X=value+diffX; Y=value+diffY; [X,Y]
Apply this to your magnify crosshair control or whatever and adjust as needed.
If you put the Magnify effect on an adjustment layer you can put this on the Center property of the Magnify effect:
L = thisComp.layer("Loupe.psd");