I also have the same problem.
I simulated nanobeam photonic crystal. In varFDTD, the resonant frequencies are different compared with 3D FDTD.
I have 3 resonance modes, for one of them the same frequency is obtained in 3D FDTD and varFDTD, but for the others, the case is totally different. To be more accurate, a 5 THz difference exists.