Shear flow orientation of nematic liquid crystals (LCs) has been investigated for two side-chain polymethacrylates having the same methoxyazobenzene mesogens but different spacers of either four (PM4MA) or six (PM6MA) methylene groups. These two polymer nematic LCs exhibited orientation behaviors distinct from each other. PM4MA arranged the nematic director in the velocity direction (the b-orientation), whereas PM6MA pointed the director to the neutral (the a-orientation) or velocity gradient (the c-orientation) directions depending on both shear rate and molar mass. Decreasing shear rate or increasing molar mass gave rise to an orientation transition from a to c. Such anomalous nematic orientation behavior is related to the presence of fluctuating smectic clusters, and explainable if fluctuations, which couple to shear flow to induce the a-orientation, have a lifetime which decreases with increasing backbone chain length so as to be sufficiently short to be averaged out under shear flow.