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What I wanted to post was this for the Pixelmon Launcher and for people using multiple displays. On a display timeout (Going to sleep) with the launcher or game up. in the AppData\Roaming\.pixelmon-beta\settings.json file the variable gets printed for "windowLeft":3907.0
So upon launching the Pixelmon Launcher the next time, the window will not appear, unless you manually go back into that file and change it over from 3907.0 to 0 then it will launch and you'll see the window fine.
I hope this will help others, as it confused the heck outta me last night. If you need anymore info let me know.