It seems that loosing/regaining focus or stopping scene causes editor to recompile scripts internally, which causes GameObject menu options to become unavailable.

Steps to reproduce:
1. Launch random Unity project
2. Select an GameObject
3. Play scene. Stop scene.
4. Right after that start toggling GameObject state (shift+alt+A)
Notice that gameObject state is not being toggled.

This might not happen at first time, but I've been able to reproduce it ~8 times out of 10.

Also I must note, that for me it took only 2-4 seconds for menu options to reappear, but it seems that for user this would take up to a one minute.

Reproduced with: 5.4.0f3, 5.4.0p4, 5.5.0b2
Not reproduced with: 5.3.5f1