We present a joint theoretical and experimental investigation to demonstrate explicitly how the combined spin-dependent interaction and the configuration interaction may affect the mixing of different spin states along various doubly excited autoionization series for Ca and Sr as energy increases across several ionization thresholds. In particular, our study has identified the inversion of energy levels between members of a number of multiplets, i.e., in contrast to the Hund's rules, due to the presence of perturber from other overlapping resonance series. We are also able to demonstrate the beginning of the breakdown of the LS coupling for resonance series corresponding to electron configurations with higher orbital angular momenta and those above the third ionization threshold.