Reproduction steps:
1. Open the attached project.
2. Check Development Build and Autoconnect Profiler checkboxes in the Player Settings.
3. Build and play the "test" scene as a Standalone.
4. Open Profiler (Window > Profiler).
5. Click on the Active Profiler button and select the Standalone player.
- Profiler doesn't show any spikes and stays at about 4000 fps (screenshot attached).
6. Click on the Active Profiler button and select the Editor.
7. Play the "test" scene in the Editor
- Profiler shows spikes (drop to 15 fps) when setting Material.shader (screenshot attached).

Reproduced with:
5.5.3p4, 2017.1.0b7
macOS, Windows