This is not surprising as supporting 2 monitors simultaneously (e.g extending your desktop as in Windows) is not supported readily out of the box.
There are a few programs that can be forced to use an alternative display (IIRC omxplayer, for example) but it is not many.
However, JamesH started creating some new firmware to facilitate this dual monitor function and is making good progress.
Please hop over to his thread here -> https://www.raspberrypi.org/forums/view ... 3&t=213854
Concerning your config.txt settings, the comments suggest that you expect the 2 sections to control 2 different monitors: VGA666 and "monitor number 2". However, the "monitor number 2" settings are also all related to the VGA666 adaptor, because they are for the dpi interface.
If you want to configure the hdmi settings, you need to additionally use hdmi_group and hdmi_mode.