Self-interaction is the process by which a microturbulence eigenmode that is extended along the direction parallel to the magnetic field interacts with itself non-linearly. This effect is particularly significant in gyrokinetic simulations accounting for kinetic passing electron dynamics. Self-interaction is known to generate stationary $E\times B$ zonal flow shear layers at radial locations near low order mode rational surfaces [Weikl et. al., Phys. Plasmas 25, 072305 (2018)]. We find however that it also plays a significant role in generating fluctuating zonal flows, which is critical to regulating transport throughout the radial extent. Unlike the usual picture of zonal flow drive where microturbulence eigenmodes coherently amplify the flow, the self-interaction drive of zonal flows from these eigenmodes are uncorrelated with each other. It is shown that the associated shearing rate of the fluctuating zonal flows therefore reduces as more toroidal modes are resolved in the simulation. In flux-tube simulations accounting for the full toroidal domain, such an increase in the density of toroidal modes corresponds to an increase in the system size, leading to a finite system size effect that is distinct from the well-known profile shearing effect.