  We study the deformation induced by fluxes and instanton effects on Yukawa
couplings involving 7-brane intersections in local F-theory constructions. In
the absence of non-perturbative effects, holomorphic Yukawa couplings do not
depend on open string fluxes. On the other hand instanton effects (or gaugino
condensation on distant 7-branes) do induce corrections to the Yukawas. The
leading order effect may also be captured by the presence of closed string
(1,2) IASD fluxes, which give rise to a non-commutative structure. We check
that even in the presence of these non-perturbative effects the holomorphic
Yukawas remain independent of magnetic fluxes. Although fermion mass
hierarchies may be obtained from these non-perturbative effects, they would
give identical Yukawa couplings for D-quark and Lepton masses in SU(5) F-theory
GUT's, in contradiction with experiment. We point out that this problem may be
solved by appropriately normalizing the wavefunctions. We show in a simple toy
model how the presence of hypercharge flux may then be responsible for the
difference between D-quarks and Lepton masses in local SU(5) GUT's.
