As an experiment I created a completely different project from scratch, recreated the heightfield load using the same source "ter" file, and the "populate now" behaved as expected, filling the area. When I compared the two projects, I noticed that the "Location" tab of the heightfield in the new project was "Position centre", while the project I'm having trouble with is "Position lower left". When I changed it to centre, the problem went away. But in the new project, when I changed it to lower left, the population button still filled the area as expected. I've added clips exported from the other project to try to find the culprit, but to no avail.
I don't really mind repositioning all the location-sensitive nodes in my project, but I'd like to know why this is happening. I'm happy to upload the tgd, but do I need to upload the heightfield file as well? It's huge, 15MB at 730x550 km.