I am not at my desktop right now so I can't show you how I did it with pictures.Here's Jason's video, go to the 4:50 mark to see his setup. As you will see, he leaves one block between the track and the portal, and they're on the same level as the portal, not one block below the portal like lenscas advocated above.
As for a time limit or "entity cooldown", perhaps that's my issue? Since it will take time for the cart to fill up before returning, this won't be an issue. However, during my testing I am trying to send the cart back and forth every 10 seconds or so. The cart goes thru the portal every time, but it never comes back. I have to go get it on the other end, and I always find it on that empty block between the track and the portal. I have no idea why Jason's setup works but mine doesn't. And neither does he. LOL
Maybe it has to do with the speed the carts have?