Thanks Andy, much appreciated. I can also load the .nii volumes manually into Matlab and calculate overlapping voxels myself, which gets around the problem too.
Can I point out one other issue that got me confused for a short while?
The 2D display flips the L-R orientation such that contact 0-3 are actually on the RIGHT electrode and contacts 8-11 are on the LEFT electrode. This threw me a bit, as the Medtronic and Boston leads are generally coded the other way around. At least here in Australasia.