We study the scalar perturbation sector of the general axisymmetric warped Salam-Sezgin model with codimension-2 branes. We focus on the perturbations which mix with the dilaton. We show that the scalar fluctuations analysis can be reduced to studying two scalar modes of constant wavefunction, plus modes of non-constant wavefunction which obey a single Schroedinger equation. From the obtained explicit solution of the scalar modes, we point out the importance of the non-constant modes in describing the four dimensional effective theory. This observation remains true for the unwarped case and was neglected in the relevant literature. Furthermore, we show that the warped solutions are free of instabilities.