Hi,
Are you using floodfill? Because that only works using the gpu engine. Substances can use a gpu or cpu engine, by default SD uses the gpu, and certain substance integrations only support the cpu engine. (I think Unreal may have an option for gpu support but I'm not sure)
You can switch to cpu in designer through tools>Switch Engine> SSE2 to check what it will look like in on the cpu engine. Differences are minor in most cases, but floodfill is not at all supported on cpu so it becomes a pixely mess. It also has some other limitations like a lower maximum resolution and a few other things that I can't quite remember from the top of my head.