I certainly don't think that War Machine was off somewhere else fighting the Chitauri during The Avengers. As far as I know, that was the sole portal, using the one and only Tesseract.
Plus, even if there was another portal somewhere, Rhodey would've most likely been killed as it took the six Avengers, the NYPD, the National Guard, and a "re-guided" nuke to win the day in New York.
I have a feeling we will get a reference to Rhodey's whereabouts during The Avengers in IM3 though. It will probably be just a passing comment about Rhodes doing his work for the USAF.
I get the distinct impression, however, that the Iron Patriot armor is going to end up being little more than a publicity move by the government in the next Iron Man movie.
It makes sense: The government wanted the Iron Man suit in IM2. Now they have one. What would they do with it? Propaganda.