Hi Graham / Kirk,
Just tested my Canon 1DX and it makes no difference which card slot you use - it will lock/tag images in either one.
When we got our first batch of 1DX bodies in early 2012, we had a similar issue in that the tags would not show up in Photo Mechanic 4.5.4.
After an upgrade to version 5 - all the tags were visible.
Suspect that Canon changed something the way an image is tagged from the Mark IV to the 1DX and the newer versions of Photo Mechanic now look for the new info.
Hope this helps,
John