I had the same problems with the magnets, before I started using Milkshape. It's how your mesh is centered. It should be standing on top of the floor grid. To correct this, after importing your mesh, before doing any rotation, go to the menu under Window and select Joint Editor. On the Joint Editor panel, under Center Point, set the X, Y, & Z values to 0 (zero). Then you can rotate your mesh and apply the magnets.
Hope this helps.
I always set x,y,z values to 0