We investigate the isospin symmetry breaking effects within a recently derived Nambu-Jona-Lasinio related model by fitting the measured pseudoscalar meson masses and weak decay couplings $f_pi$, $f_K$. Our model contains the next to leading order terms in the $1/N_c$ expansion of the effective multi-quark Lagrangian, including the ones that break the chiral symmetry explicitly. We show the important phenomenological role of these interactions: (1) they lead to an accurate fit of the low-lying pseudoscalar nonet characteristics; (2) they account for a very good agreement of the current quark masses with the present PDG values; (3) they reduce by $40%$ the ratio $epsilon/epsilon$ of the $pi_0-eta$ and $pi_0-eta$ mixing angles, as compared to the case that contemplates explicit breaking only in the leading order, bringing it in consonance with the quoted values in the literature. The conventional NJL-type models fail in the joint description of these parameters.