I downloaded the test.rwp after reviewing your post on the test and here are my best guesses and a solution as to why your test scenario didn't work.
If I remember correctly it was the UP train with the path failure, right? I already saved my version and quit Railworks so I can't go back and look. The failure in this scenario wasn't the priority but rather your trying to put two AI trains in the same yard. Let's get to some basics first. This is going to go way beyond class priority but it should help you appreciate why a simple looking scenario can become so complicated.
The yard is protected on both ends by signals and while it is a multi-track yard, remember, to the signals it's still a single piece of track. So any blockage or traffic in between the two signals would normally give you a red. And in this case, I believe that's what is the problem here. Granted the signals are the E type meaning they ignore that there's traffic beyond the signals - but only to a degree. Let's remember this as layer 1 as Andy referred to in his post where scenarios are complicated because layers of intelligence are at work here.
The second and probably more imporant layer here is the pathing. Both players are ending up on the same single strip of track we call the yard. So as far as the pathing is concerned you have two trains occupying the same block. In my own scenarios where I tried to include the player train and an AI train in the yard at the same time, wouldn't work. Whereas the E signals suggest this is not a problem (and maybe only with rollingstock!) the pathing overrules.
Pathing is key. And note it didn't matter when the pathing obstruction occurred, that it does, you're three strikes and out. This becomes problematic because you must learn to think through and anticipate the pathing problems. Pathing is more complicated in Railworks than MSTS because you don't have ultimate control over any of the train paths. You should. The AI is constantly trying to be clever and find a clear path much like you saw in the old Transport Tycoon games or some of the Railroad Tycoon games. This creates an unpredictability and it muddies up the solution because of it and only adds further to the confusion for how to get a scenario to work.
But ultimately the goal is to get the scenario to work, right? So I did this:
testrw1.jpg
By changing the ultimate destination to Portal N for the UP train, the scenario should work. I didn't test it though I should've. Just cause everything looks free and clear now it doesn't mean it works, totally. I would also say that any priority used, like standard over other freight would have given you the same results. That's something you'll have to try though to be certain.
Hope this helps.
Rich