A system of D1- and D5-branes with a Kaluza-Klein momentum is re-investigat
ed using the five-dimensional U-duality group E6(+6)(Z). We show that the r
esidual U-duality symmetry that keeps this D1-D5-KK system intact is generi
cally given by a lift of the Weyl group of F4(+4), embedded as a finite sub
group in E6(+6)(Z) We also show that the residual U-duality group is enhanc
ed to F4(+4)(Z) when all three charges coincide. We then apply the analysis
to the AdS(3)/CFT2 correspondence and discuss that among 28 marginal opera
tors of CFT2 which couple to massless scalars of AdS(3) gravity at the boun
dary, 16 would behave as exactly marginal operators for generic D1-D5-KK sy
stems. This is shown by analyzing possible three-point couplings among the
42 Kaluza-Klein scalars with the use of their transformation properties und
er the residual U-duality group.