To reproduce:
1. Open the attached project;
-note: Do not change Editor Layout.
2. Load "Test" scene;
3. Align the scene view camera toward the negative Z-axis by clicking the blue Z arrow;
4. Ensure the scene view camera is orthographic;
5. Click three times on the region where the three cubes overlap;
6. Align the scene view camera toward the positive Z-axis by clicking the arrow opposite the blue Z arrow;
7. Repeat 5th step.

Expected result: distance to the Scene View Camera is not ignored in the Orthographic mode when using custom Editor Layout.
Actual result: distance to the Scene View Camera is ignored, clicking a region where three cubes are overlapping cycles through the objects from the furthest to the closest when Scene View Camera is aligned toward the negative Z-axis.

Workaround: change Editor Layout to Default.

Reproduced on versions: 5.5.5f1, 5.6.3p4, 2017.1.2f1, 2017.2.0f3.

Not reproducible on: 2018.2.0a6.