Maybe the thing that made the difference was not which side was "rubbed vigorously". Those who did the rubbing were probably mostly right-handed. So rubbing on one side may have been against the lay of the hair, and been uncomfortable.
http://www.sciencedaily.com/releases/2010/12/101213122001.htm
ScienceDaily (Dec. 13, 2010) — Certain events experienced at the moment of birth have consequences on the emotional reactions of animals at an adult age. Researchers from the Laboratoire d'Ethologie Animale et Humaine (CNRS/Université de Rennes 1) have tested the effects of unilateral tactile stimulation on newborn foals. Their results show that animals handled on their right side at birth avoid contact with humans more often than those stimulated on their left side or not at all. Published in Biology Letters, this work raises questions on the organization of neonatal care in animals and humans.
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The ethologists tested the consequences of unilateral tactile stimulations on 28 newborn foals: 10 of them were handled just after birth on their right side (the newborn foals were "rubbed" vigorously for one hour on a single side), 9 others on their left side, while the remaining 9 were not handled at all. The researchers then observed medium-term effects: the reactions of foals to a human approach, when they were 10 days old, differed according to the side stimulated at birth. The right-handled animals fled at the approach of humans more often than the left-handled or unhandled foals.
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