OK, solved this, although it seems a little obtuse to me, to say the least.
Prior to saving the project file (or at least before running it from the command line) you need to:
a) You have to run the compare - BUT.. the comparison needs to pick up some differences
b) As it has picked up some differences, when the results are shown, in the heading row, you need to check the tickbox between the 2 "Object Name" columns, and then
c) save your project.
Though the project file is a text / XML file, doing the above steps adds some encrypted guff in the file, that seems to make it work - i.e it's not simply changing one of the xml values to True that was False.
Hope this helps someone... There must surely be a better way of fixing this...