The effects of numerical viscosity, subgrid scale (SGS) viscosity and grid resolution are investigated in LES and VMS-LES simulations of the flow around a circular cylinder at Re=3900 on unstructured grids. The separation between the largest and the smallest resolved scales in the VMS formulation is obtained through a variational projection operator and finite-volume cell agglomeration. Three different non-dynamic eddy-viscosity SGS models are used both in classical and in VMS-LES. The so-called small-small formulation is used in VMS-LES, i.e. the SGS viscosity is computed as a function of the smallest resolved scales. Two different grid resolutions are considered. It is found that, for each considered SGS model, the amount of SGS viscosity introduced in the VMS-LES formulation is significantly lower than in classical LES. This, together with the fact that in the VMS formulation the SGS viscosity only acts on the smallest resolved scales, has a strong impact on the results. However, a significant sensitivity of the results to the considered SGS model remains also in the VMS-LES formulation. Moreover, passing from classical LES to VMS-LES does not systematically lead to an improvement of the quality of the numerical predictions.