Good to hear Geo,
Apologies for the prolonged absence, my poor old laptop fell over in a rather major way so I had to get another
Then I ended up playing The Witcher 2 to test new machine (my old one stuggled, this beastie made it fun again).
Back to business at hand though, the general commands on the left (behaviour, how much power to assign to systems) don't affect the command, but all the manual commands along the centre (the bit to turn on specific devices or target weapons, etc) and those on the right interupt the tick so we proceed to the last set destination.
So I'd go along with your assumption of manual command interuption is correct.
So the question then becomes 'How to capture these manual events?' if it's at all possible.