Reproduction Steps:
1. Import attached project.
2. Open "TimeTest" scene.
3. Select "Test Object" in Hierarchy.
4. Move it around in the Scene.

Expected Result: Time and FixedTime do not progress.
Actual Result: Time and FixedTime progress.

Reproducible with: 5.5.2p2, 5.6.0b11, 2017.1.0a3
Not reproducible with: 5.4.5f1
Regressiong introduced in: 5.5.0f2

Note #1: Bug appears even without "runInEditMode = false".
Note #2: runInEditMode is not available in 5.4. However, the bug does not appear in that version either way.

SOLUTION: Check Application.isPlaying in your code whenever you don't want to use time in edit mode.