Here is what I did to fix it. Open up your GPU app. nVidia control panel or whatever AMD/INTEL has. Turn off all monitors except for the monitor you want as primary. Fire up OBS. Delete your display capture and add a new one. Set it to automatic and it should already be on your primary monitor since it's the only one you have on. While OBS is still up, turn on your other monitors within your apps and apply the settings. Close the app. OBS should still be displaying your primary monitor as the capture. Close OBS and restart it. The settings should stick for you.