We examine the implication of heavy quarkonium decays for estimating the light quark masses, particularly the mass ratio m(u)/m(d), at next to leading order in the quark mass expansion. It is observed that, due to instanton effects, some matrix elements which have been ignored in previous works can give a significant contribution to decay amplitudes, which results in a large uncertainty in the value of m(u)/m(d) deduced from quarkonium phenomenology. This uncertainty can be resolved only by a QCD calculation of some second order coefficients in the chiral expansion of decay amplitudes.