It just requires a highpoly OBJ with the polypaint data, no UV's or textures needed. It will also only transfer the RGB polypaint values, not any materials in zbrush.
This isn't a common issue. I'd be inclined to look into the source mesh or the export rather than painter's import process. Are you going to fbx or obj?
In Marmoset, if it's missing pieces.. either the normals are inverted for that section, it's 5+ sided poly, or when you exported it as an .obj you forgot to check all the options as positive.
When you export the lowpoly OBJ, are you including vertex normals in it? In Xnormal, when you add the lowpoly model, are you setting it to use Exported Normals?
Reset your model's transforms and scale, export as OBJ, make sure all input textures are the same size, and try creating a new project to see if this persists.
Add a .obj option as well to cover a broader sweep of 3D software/middleware solutions out there, because universally the ubiquitous .fbx format doesn't always work.