Is this the Heightfield Generate? I can see why this is causing a problem.
Before this feature was added, most people were reloading their projects and didn't know why the terrain was missing. It must be off by default so that an ungenerated terrain won't be generated when the project loads, and we turn it on automatically when someone generates the terrain because most people are not going to remember to check it every time.
Your situation is a bit different because you need it to generate in a specific order. I was wondering if you could just click Abort when it loads, but it seems to not allow that, and that's a bug. I'll see if I can fix that.