Intersecting D-brane models and their T-dual magnetic compactifications yield attractive models of particle physics where magnetic flux plays a twofold role, being the source of fermion chirality as well as supersymmetry breaking. A potential problem of these models is the appearance of tachyons which can only be avoided in certain regions of moduli space and in the presence of Wilson lines. We study the effective four-dimensional field theory for an orientifold compactification of type IIA string theory and the corresponding toroidal compactification of type I string theory. After determining the Kaluza-Klein and Landau-level towers of massive states in different sectors of the model, we evaluate their contributions to the one-loop effective potential, summing over all massive states, and we relate the result to the corresponding string partition functions. We find that the Wilson-line effective potential has only saddle points, and the theory is therefore driven to the tachyonic regime. There tachyon condensation takes place and chiral fermions acquire a mass of the order of the compactification scale. We also find evidence for a tachyonic behaviour of the volume moduli. More work on tachyon condensation is needed to clarify the connection between supersymmetry breaking, a chiral fermion spectrum and vacuum stability.