We numerically investigate the dynamics of a long window junction under the influence of a constant current bias, and intermediate damping in the junction area. The current voltage characteristics are calculated for various sizes of the passive region extension w′ and different thickness of the isolating layer in the idle region. The existence of the idle region influences the fluxon solutions, and consequently the I–V characteristics, causing the fluxons to increase their critical velocity above the Swihart velocity in the window and to radiate by way of the Cherenkov effect as they move in the junction. The fluxons become phase locked with the Cherenkov radiation, and this is reflected in the I–V curve as very strong resonances at relatively high velocities.