also the duration of the events should be the opposite
D.trials.events(i).duration = sFileIn.events(iEvt).times(2,iOcc) - sFileIn.events(iEvt).times(1,iOcc);
and not
D.trials.events(i).duration = sFileIn.events(iEvt).times(1,iOcc) - sFileIn.events(iEvt).times(2,iOcc);