I read on a sport touring message board that the large JC whitney case worked with givi racks. I tried the same thing as you, SW motech racks with the JC whitney case...didn't work for me, either. I ended up returning the JC whitney case and buying a givi case.
The JC Whitney case *probably* would work with the SW Motech racks with Givi adapter plates with slight modification to the JC Whitney case (ie - shaving the slots at the rear of the case a bit). The latch is the same, and the distances between the latch and the rear slots is the same, but the rear slots are slightly different (I can't remember...they were either a bit too narrow, or a bit too wide or something).
Or, you could permanently bolt the adapter plate that came with the case to the rack.
The Givi brand racks must be slightly different, because I read from several posters that they made the givi brand racks work with this case with no modification.