There are 3 different bugs in this report. I filed them together as the underlying code or problem might be the same. There are 3 main issues:

1. Geometry that has no additional vertex stream, will get affected if the same geometry is painted with additional vertex stream
color, even if they're on a different scene.
2. Albedo in Realtime GI is confused whenever there's geometry with Additional vertex Stream Color painted on them.
3. There are artifacts in Realtime GI results if a geometry has additional Vertex Stream color painted on them.

To reproduce:

1. Download attached project "VertexStream_Issue.zip" and open in Unity
2. Open "VertexPaintScene_Vanilla" scene and move the light around
Note: This scene is plain vanilla - it does NOT count additional vertex streams (no painted vertexes). Also, you'll see that the scene is properly illuminated with white.
3. Open "VertextPaint_Playground" scene and move the light around
Note: Move the light around. You'll see that the scene is properly illuminated with whatever albedo the light is close too. No problem here.
4. Open "VertexPaintScene_Vanilla" scene again
Note: Observe that it has the same "stripped" albedo as the "VertextPaint_Playground" scene
5. Open "VertextPaint_Playground" scene and move the light around
Note: Observe that there are no reflections while moving the light around
6. Generate Lighting
Note: Observe that it uses the Albedo from the "VertextPaint_Playground" scene again and note how the reflections match the "stripped" colors from the "VertextPaint_Playground" scene, instead of the solid colors of the "VertextPaintScene_wAdditionalVertexStream" scene. Also, you can see artifacts on the edges of the planes

Notes:
- Additional Vertex Stream color is added/painted using the VertexPanterPro add-on
- This happened on the same Unity Session
- Restarting Unity on a precomputed (RealtimeGI) looks fine, however, upon baking, everything gets messed up

Reproduced on Unity 5.6.4p3, 2017.1.2p3, 2017.2.0p2, 2017.3.0b10 and 2018.1.0a5