I have a xubuntu 12.04 setup with NVIDIA GT610 proprietary driver, TV with HDMI and vga monitor. it worked perfect with 11.10 and vlc 1.1.X with 60Hz on VGA and 50 Hz on TV.
Now with 12.04 and 2.0.3 vlc i can't have different refresh rates, video get totally messed up, tearing, jerky, out of lipsync. Using 60 Hz on both monitors works with the inherent problems of 50 Hz video on 60 Hz monitor, regular jerking. Same at least wit ATI adapter.