I too am having this problem: no time/frame count display in the toolbar.
I have tried: launching Motion and deleting preferences; resetting PRAM; resetting SMC; deleting and reinstalling Motion; removing third-party Motion projects; reinstalling El Capitan; validating fonts; deleting Motion from Time Machine backup process; and changing Energy Saver settings. Nothing works.
The time/frame display will appear, sometimes remain for a day or two, and then be gone again.
However I have discovered an easy work-around which doesn't require restarting the Mac: simply log out (Apple Menu > Log Out) and immediately log back in. But again: it's only a temporary fix. The time/frame display will be gone the next time Motion is launched or shortly thereafter.
Thankfully I don't have to rely on Motion too often.
About the only thing I haven't tried is a different User account. Has anyone gone down that path?
Running OS 10.11.6. Motion 5.2.3. Mac Pro (late 2013). Apple Thunderbolt Display.