The dielectric and structural properties of the S=1 kagome antiferromagnet KV3Ge2O9 are examined. The low-temperature structure below 50 K is orthorhombic with a typical correlation length of 8 nm. While the high-temperature hexagonal phase can be considered C-centered orthorhombic, the C-centered symmetry is broken below 50 K. The low-temperature symmetry does not support the simplex solid state, which is the theoretically expected ground state for the S=1 kagome lattice. Above 60 K, incommensurate lattice modulation is observed. The lock-in transition suggests that the origin of the orthorhombic deformation is the development of a short-range magnetic ordering.