To reproduce:
1. Open the attached project;
2. Open "direct_shadows" scene;
3. Open Lighting window;
4. Generate lighting (make sure Baked Data is cleared);
5. Clear Lighting Data;
6. Tick Prioritize View (Lightmapping Settings > Prioritize View);
7. Generate lighting.

Expected result: After baking lighting, both results look the same.
Actual result: Supersampling renders indeterministic results with direct samples.

Workaround:
1) Create new Lightmap Parameter (Lighting > Lightmapping Settings > Lightmap Parameters > Create New...);
2) In the Inspector Window, change Anti-aliasing Samples to 1;
3) Repeat steps 3-7 from reproduction steps above.

Reproduced on versions: 5.6.3f1, 2017.1.0p2, 2017.2.0b5, 2017.3.0a2.