Thanks Anderton and dcumpian,
I probably didn't make it clear that Sonar X3 Producer and the trial of Sonar Platinum both worked identically and correctly with respect to this issue. It was only when I updated the Platinum trial to version 2016.03 yesterday that these problems started.
So these issues are new with version 2016.03 and weren't there for the previous version. The settings imported from X3 by the initial version of the Platinum trial worked fine and the problems only surfaced when going from Platinum (2016.02 I'm guessing) to 2016.03 using command centre.