One customer of us had a similar kind of problem. In that case the building itself is not far from origin. I don't know what has been happen the the ArchiCAD file, but after some modifications the windows were located very far away in IFC file generated from the ArchiCAD model.
I found a workaround for to avoid the problem. Not an elegant one, but it works
Create another ArchiCAD model
Create floors in the same elevations than in the original model
Open the original model and copy all components in one floor
Paste the components to the same floor on your new model
Replace for all floors
And in the end you can create IFC file -> Windows are located in correct places.