Re: Flash player full screen mode broken with nVidia?
You can try disabling the internal panel in nvidia-settings. Or change the MetaMode in your configuration to not include your DFP. As gbil said, Youtube computes the aspect ratio of the fullscreen video using the aspect of the total desktop area rather than just the display you're maximizing on, resulting in this problem. I'm assuming the AMD configuration you were referring to was single-display?