Sorry - I feel your pain. When I discovered ITA Matrix it seemed great, but I am in the group that likes to do my own bookings, and the only way to try to get those fares is via a travel agent.
In my understanding, essentially what ITA matrix does is search the various "official" airline databases to see what the lowest technically-available fares are. But the ability of online sites to find and offer these same fares is VERY patchy. So most people will advise you to "find a good travel agent".
If you do that, then please be aware that the travel agent has to make a living too, so I would expect to be paying them more than the ITA fare.
But anyway, as in all fare searching, try a variety of sites to see if they offer what you are seeing via ITA. Try google flights and hipmonkey for starters......