I would trust the surface parameters over the trajectories.
The flow trajectories are back-calculated from the mesh through points picked out by the software on the chosen face. There are also a limited number of trajectories, so that's why you're only seeing them from certain inlets.
If you want to see how the trajectories interact, you could do 6 studies (one for each inlet) and color each one of them a different solid color. Pick ones that will stand out from each other: red blue yellow etc... Make sure you pick the same number of trajectories for each calculation. That will allow you to see how the six inlets mix and flow through your manifold.
what you get in a flow trajectories plot depend on what you pick for the source and its mesh properties amongst other things... You can get really good looking ones if you put in an pick surfaces at each outlet and ask for the same number of low trajectories from each. This would look even you the flow were vastly different. Hopefully you get the point.