Handles not appearing in scene view when in tool mode

1. What happened

When using e.g., BoxBoundsHandle via a tool mode (e.g., edit collider) Handles are not drawn (n.b. not to be confused with Gizmos). When using it not via a tool mode (e.g., ParticleSystem shape module) they appear fine. Reverting the layout back to default makes the problem go away. I was able to reproduce the problem in 5.5.0, 5.6.0, and 2017.1b3

2. How we can reproduce it using the example you attached

- Open the attached project
- Create a cube
- Try to enter Edit Collider mode from the Inspector
- You should see the wireframe (Gizmo) cube, but no control handles
- Create a Particle System
- Expand the Shape module in the inspector and go through different shapes (e.g., cube); you should see both wireframes and control handles
- Revert the window layout to default and repeat steps above; everything should work as expected now