I've just been trying to book an itinerary that showed up on Matrix similar to that, and because I needed a stopover that would result in one outbound segment entirely outside Canada on a non-AC airline, I expected the multi city would not book it online, so I emailed a travel agent. For a whole day, I kept getting this "married segment married segment" klaxon in response, and a "your ticket will either cost 2 1/2 times the Matrix price or have 10 hours of air time at 0% AQM." However, a second day of emailing a different agent produced the flights I wanted, all earning AQM, within an exchange rate's fluctuation of the price Matrix found. Matrix is just smarter than the average TA, I think.