  We analyze CP violation and Flavor Changing effects in a general Minimal
Supersymmetric extension of the Standard Model with arbitrary non-universal
soft-breaking terms. We show that, in this conditions, large FCNC effects are
naturally expected in the Kaon system, even in the absence of quark-squark
flavor misalignment. On the other hand, the B system is only sensitive to new
supersymmetric contributions if the non-universality implies, not only
different soft term for the three generations but also the presence of a
quark-squark misalignment much larger that the corresponding CKM mixing. The
only exception to this rule are processes where the chirality changing
contributions proportional to tan beta are leading (for instance b -> s gamma).
