I’ve encountered similar issues with non-combined meshes. It’s not merely the lightmapping. If you look at the doc pages on skylight, there’s a discrepancy in how the lighting appears in a scene with the cubemap being based on the captured scene and with the cubemap being based on a specified cubemap. The two options in skylight can be rather different in lighting a scene, whether the lightmapping is 100% correct or not. The ‘captured scene’ option actually captures a cubic projection of the background AND the active scene (where your structures and meshes are), and reprojects that as lighting. It’s obviously doing some calculations and transforming the data to lighting. However, the ‘specified cubemap’ option uses the data (color information, and differences in light/dark, and more) to light a scene. This can result in blemishes and shadows being placed in areas they’re not supposed to be, depending on which option is selected and what is in the image (captured scene or a picture / cubemap that is not the scene itself but an isolated image that data is being pulled from). What is your skylight setting for cubemap? What is the skylight’s mobility?