Being curious as to what this "rocking motion" meant, I scoured the web for articles that explain the same. Most of the articles mention that this has something to do with the Kundalini Energy arising. Some say it's a natural thing that happens - The body makes some adjustments to the system during these motions - adjustments for the better.
Some say, it's about clearing energy pathways or chakras. So below I list a few articles that I think are relevant to this upper body involuntary movement stuff:
1) Kundalini Awakening
2) Spontaneous Movement
3) Odd rocking motion
5) Raw foodie's story
7) Ecstatic Movement
8) Effects of meditation
9)More on tingling/crawling sensations
I think this upper body movement during meditation hardly affects my meditation. I am definitely intrigued by it, but keeping with the spirit of meditation, I just observe it as a phenomenon that's happening to me.