Intermittent Harmonics, Is there a physical explanation?
You have guessed it right. But before an explanation, you should make sure that your measuring setup is not the cause of this observation. 

The fact that your fundamental frequency is 0.7 Hz. does not mean that you should see all harmonics of that frequency at 1.4 Hz., 2.1. Hz, 2.8 Hz. etc...  

And furthermore, even if you would see those harmonics, their weights would most typically be different as suggested by the continuous-time Fourier series analysis of periodic waveforms.

The physical explanation is that your mechanical rotating system as a whole can be (approx) modeled as an LTI system with a self-frequency response composed of resonating or damping frequency modes... 

And it seems that at 2.1 Hz., the system is not able to vibrate enough, some damping must be happening.

Nothing further can be stated at this point with the given information.