Yes, of course, a forest or jungle tile only counts as and acts like a road when it's within your civ boundary. But the problem I was running into, was entirely within my Iroquois civ boundary- I'd built a road from my capital to a nearby city, and it consisted of six tiles: a forest, a plain with a road chunk on it, another forest, another plain with a road chunk on it, and then two forest tiles on the far end. This worked fine and provided fast travel and a trade route between the two cities all the way up until I updated the two non-forest plains road chunks to railroad- after that, even though the trade route remained functional, every time I tried to cruise a unit over that stretch, they'd stop and get slowed down and hung up and wander off the path as soon as they got to the railroad chunks- as if it was broken there or something. No idea why, just mo' buggies, I guess.