Whenever a ROM is loaded the front end goes away and you see Windows for a second before the ROM starts. Is there a way to hide this this?
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No, it’s just a thing that happens when the context gets torn down to create the new context. You can, however, set a black background and get rid of all of your desktop icons to minimize the intrusion.
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Alright, thanks. 
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You could look into RocketLauncher as that program allows for fade screens but tou would then need to use a dedicated frontend like RetroFE, Hyperspin or LaunchBox to browse and select games. Probabky overkill for what you want.
@hunterk it would actually be good if Retroarch held focus during this process. I’m convinced that the weirdness I see in Steam Big Picture Mode is because of this (Retroarch drops focus, the button press that launched the game in RA leaks through to Big Picture mode, which spawns another instance of Retroarch, sometimes at least).
@daninthemix The problem is that the window itself is destroyed, so there is nothing to focus on until the new one is created. This behavior is fairly deeply tied into how RA works internally, so I don’t think it would be an easy change.