Steps to reproduce:

1. Open Unity on OSX;
2. Create new project;
3. Import attached 'testBreakpointCursorBug.unitypackage' package;
4. Open 'test.unity' scene;
5. Select 'FPSController' gameobject in the Hierarchy;
6. Click on the cogwheel First Person Controller (Script) in the Inspector -> Edit Script;
7. In MonoDevelop set breakpoint at any line within Update() or FixedUpdate() methods (for instance, line 66 - if (!m_Jump) );
8. Attach Editor process to MonoDevelop;
9. Enter Play mode;

10. Notice that breakpoint behaves correctly, stopping at the correct line and Editor freezes as expected;

11. Now click on Editor window;

Actual result:
Spinning cursor freezes - it stops reacting to any mouse movement. In some cases it disappears. See attached gif video.

Regression introduced somewhere in 5.3.0.

Expected result:
Spinning cursor should not freeze or disappear after clicking on Editor window with reached breakpoint.

Workaround is to switch windows by using cmd+Tab. In this case cursor appears and becomes active.

Notes:
- Reproduces on OSX (10.11.1 checked);
- Reproduces on 5.4.0a6, 5.3.1f1, 5.3.0f4;
- Doesn't reproduce on 5.2.2p4;
- Reproduces for MD 5.9.6;
- Doesn't reproduce when setting breakpoint in Start() method.