Alright when your using the portal do you just drive it in or do you give it any particular commands. when i normally use the portals i use the Drive To Command and select the name or number of the portal. unless there is a track issue they normally drive in without a hitch.
regarding the the time issue you speak of you can during the setting up in surveyor adjust the time limit it will take before the trains return. also you can adjust the loading or unloading of the train through the portal as well. its just a case of experimenting. if your wondering how to change the properties of the portal you need to select the "?" and have the portal in map selected, and a screen will appear allowing you to adjust the settings.
hope this helps you
Cheers
Ghosty