Just off the top of my head, I'd guess the problem might be that the train cars you're selecting to appear, might not be compatible with TS2009. I've had problems where I just randomly selected a certain loco and it wouldn't appear, and that was the problem. The only way to be sure is, in Surveyor, open the train placement tab, and select something and actually place in on the track. If that works, then try coding the same loco to appear in the portal.
The portals I can assure you, DO work. I have several routes that use portals thaat I brought over from TRS2006, notably Summer Lake Valley, and Port Ogden and Northern 1a, plus a route of my own that I'm tinkering with and I have had no problems getting trains to appear, as long as '09 can recognise them.