The AI are not always as dumb as they seem. In this case there may actually be a problem.
Check that you don't have any broken track, or mispointed direction markers. This will make the AI sit there and wait. To check for broken track, either drive the stopped train manually, or go into Surveyor, and walk the line slowly while looking at the connections.
Direction makers can be tricky because you may have it incorrect, but in your mind you may see it as the opposite. You need two markers one for one track, and one for the other if you have a two-track route. Also Direction Markers show the direction you want the trains to go in. If you have one that's backwards on the route for your train, this will cause them to stop.
My gut feeling though it's your signalling that's causing the problems so make sure you're line is properly signaled otherwise the AI will sit there until the track ahead is clear. Refer to the different threads on signalling.
In general when I add in portals, I setup two - one for spawning trains and the other for accepting them back in. I also have at least a baseboard of track between the portals and the line that they will traverse. This gives the AI plenty of time to throttle down before they reach the main so they don't go blasting through everything blindly until they gather their limited brains.
If my portals lead down to single track, which in many cases they will, I setup the junction just like any other with the proper speed markers and signaling. By the time the AI have reached this point, they are at the proper speed anyway, and are ready to join the rest of the population on the route.
John