  Non-perturbative superpotential cross-couplings between visible sector matter
and K\"ahler moduli can lead to significant flavour-changing neutral currents
in compactifications of type IIB string theory. Here, we compute corrections to
Yukawa couplings in orbifold models with chiral matter localised on D3-branes
and non-perturbative effects on distant D7-branes. By evaluating a threshold
correction to the D7-brane gauge coupling, we determine conditions under which
the non-perturbative corrections to the Yukawa couplings appear. The flavour
structure of the induced Yukawa coupling generically fails to be aligned with
the tree-flavour structure. We check our results by also evaluating a
correlation function of two D7-brane gauginos and a D3-brane Yukawa coupling.
Finally, by calculating a string amplitude between n hidden scalars and visible
matter we show how non-vanishing vacuum expectation values of distant D7-brane
scalars, if present, may correct visible Yukawa couplings with a flavour
structure that differs from the tree-level flavour structure.
