A while ago, when looking for flights from BOS to SAN the ITA Matrix would not hand out the cheapest result either - until I added "UA1-9999 UA1-9999 UA1-9999" to the options. With two stops, I could get there quite cheap *and* faster.

I did the same search several times over a couple of weeks, it was always the same situation. Only with the abovementioned options I got the ideal result (I think X X worked as well at some times, but not always).

I thought the result was supressed because it was a more cumbersome trip (two connections). Other flights by the same airline (UA) where included. But the complete exclusion of Aeroflot from NYC->VIE, while it being the cheapest of all options, is even more weird.