Currently (version 0.56.1), if you have Witcher 3 installed through Steam, NMM is unable to instantly retrieve the game folder if it's not installed in the Steam default folder: you either need to wait for the full scan or select it manually, but make sure to select "The Witcher 3" folder, not the witcher3.exe path.
eg.:
d:\games\Steam\steamapps\common\The Witcher 3 - is good
d:\games\Steam\steamapps\common\The Witcher 3\bin\x64 - is wrong