prefab when dragged on scene is not where its saved to be

I instantiate prefabs into the sword hand, and the prefabs saved rotation and position etc is used and it normally works fine, since i have updated to 4.5,now, i.e, when i try to position a sword i save it as prefab, when i drag the prefab back on the scene, its not where i just saved it to be, as it usually would be, ive tried using an empty gameobject as parent and set it up that way, and i have the same problem, and i cant get it to work
this is crucial for my game, any one have any ideas whats going on?

Object location, from the original location, i move it and save it to the position seen in the screen shot below

than when i drag the prefab out its in a different position, as shown below

Hi EntropicJoey1, as Wijesijp said in a comment, yes you must drag it into the Hierarchy pane, if you try draging it directly into the scene pane, it changes the x,y,z coordinates to where you dragged it.

If you take it straight to the Hierarchy pane it keeps your coordinates how they where when you made it a prefab.

Hope this helps.