We study BPS excitations in M5-M2-brane configurations with a compact transverse direction, which are also relevant for type IIa and IIb little string theories. These configurations are dual to a class of toric elliptically fibered Calabi-Yau manifolds X_N with manifest SL(2, Z) × SL(2,Z) modular symmetry. They admit two dual gauge theory descriptions. For both, the non-perturbative partition function can be written as an expansion of the topological string partition function of X_N with

more »

... to either of the two modular parameters. We analyze the resulting BPS counting functions in detail and find that they can be fully constructed as linear combinations of the BPS counting functions of M5-M2-brane configurations with non-compact transverse directions. For certain M2-brane configurations, we also find that the free energies in the two dual theories agree with each other, which points to a new correspondence between instanton and monopole configurations. These results are also a manifestation of T-duality between type IIa and IIb little string theories.