I had the exact same problem... the problem is basically shadowplay gets confused and kinda like combine the desktop recording and the game recording,, the way to fix it is..
make sure you always start/stop recording ON DESKTOP SCREEN, save last few min ON desktop screen... for example if someone RDM you.. and you wanna save last 5-20 you go to desktop screen by pressing ALT+TAB, windows key+D, or ALT+CTRL+DELETE -> task manager.. just anyway to get you on desktop screen then save and go back on game,, the video will save where you want to save it and it will play fine.... you dont need to download anything to reinstall anything just try this and let me how it turned out.