If super-Yang-Mills theory possesses the exact conformal invariance, there is an additional modular invariance under the change of the complex bare charge τ = θ 2π + 4πı g 2 −→ − 1 τ . The low-energy Seiberg-Witten prepotential F (a), however, is not explicitly invariant, because the flat moduli also change a −→ a D = ∂F /∂a. In result, the prepotential is not a modular form and depends also on the anomalous Eisenstein series E 2 . This dependence is usually described by the universal MNW modular anomaly equation. We demonstrate that, in the 6d SU(N ) theory with two independent modular parameters τ andτ , the modular anomaly equation changes, because the modular transform of τ is accompanied by an (N -dependent!) shift ofτ and vice versa. This is a new peculiarity of double-elliptic systems, which deserves further investigation.