Recently {[}N. E. Mavromatos and S. Sarkar, New J. Phys. 10, 073009 (2008); N. E. Mavromatos, S. Sarkar, and W. Tarantino, Phys. Rev. D 80, 084046 (2009)], we argued that a particular model of string-inspired quantum space-time foam (D-foam) may induce oscillations and mixing among flavored particles. As a result, rather than the mass-eigenstate vacuum, the correct ground state to describe the underlying dynamics is the flavor vacuum, proposed some time ago by Blasone and Vitiello as a description of quantum field theories with mixing. At the microscopic level, the breaking of target-space supersymmetry is induced in our space-time foam model by the relative transverse motion of brane defects. Motivated by these results, we show that the fl...