Hi davidrichens,
Baking VRayLightmaps is incompatable with Standard materials, and will produce something like a CompleteMap as you said. Ideally you should only be using VRayMtl materials.
If that would be too time consuming, the quick and dirty way is to to go to Render Settings, VRay Tab, VRay Global Switches rollout, then add a 50% gray VRayMtl in the material override slot. After that, click on exclude and exclude any transparent objects from override. This will keep windows and similar objects from going opaque during the bake.
Any object affected by the override will be able to produce proper light maps. The main drawback of this method is that it reduces the accuracy of the GI solution by removing any variation that comes from surface color. EG. light bounced off a bright red wall would become red and add a slight red tint to any nearby surfaces.
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