The head bobble is a widespread gesture in South Asia that is notoriously difficult to translate into Western body language. Used to express uncertainty, interrogation, reticence, assent, and a variety of other ideas, it's use has famously been used as a litmus to determine whether a person was raised in a South Asian culture.
According to Rinda Sama, the Indian Head Bobble first originated when India was under The Indian Monarchy. When replying to the Rulers of India (both British and Indian) the people were reluctant to say no due to the often violent responses of their country’s leaders. So they would tend to sway and shake their head back and forth to let them decide for themselves what they wanted it to mean.
While this may not be entirely factually true, the meaning that it's an ambivalent response is accurate. I've found it difficult to find any other cultural origin for the behaviour so I'll leave this historical interpretation as it is; an interpretation.
Also, I've personally noted that the bobble is more prevalent the further south you go in India.
Can you provide an example? I can't visualize what you're describing.