Hi Jeremy,
it seems to be an OS issue more than a "real problem",
I mean there's nothing wrong with both my macbook and my external monitor,
it seems more like an OS "bug" that happens every time I watch an app in fullscreen mode,
which makes the other monitor go black (it happens with both integrated retina and the external one, according to where this app is sent full screen at that moment), and by "black" i don't mean completely inactive or disconnected, but active and well working just for my cursor on a black background, so that if I move one element of the full screen app from its actual monitor to the other (like for example a single browser tab) the second monitor can show this tab well, but again sends the other monitor black, something like "you can't have 2 monitor displaying apps at the same moment if one of these is watched in full screen mode".
The only exception is given by Youtube fullscreen mode, this is the only way it can work for me so far... but if i send in fullcreen the browser instead of the single youtube video, it goes as described here above (makes the other monitor black)