Right click each executable then click on properties then click the second tab which is 'compatibility' at the bottom check 'run as administrator' then click ok. Set MO and F4SE to run as admin, to do this find their executables, F4se is likely steam/steamapps/common/Fallout 4/f4se_loader.exe and MO you should know where this is installed at this point. Turn off your antivirus, if this fixes it you will need to add an exception in your AV firewall for F4SE and possible MO. Restart your computer, by now you probably have been installing mods, and trying to launch the game multiple times, restarting will get rid of any lingering 'dummy' executables that failed to launch which you may see in task manager. If F4se loads but not with MO still then try some of these starting with the most obvious. In this situtation verify that F4 is up to date along with F4SE, sometimes F4SE updates come out a day or so after F4 updates which may cause launch issues. If it doesn't load then its likely nothing to do with Mod Organizer. This is usually steam/steamapps/common/Fallout 4/f4se_loader.exe. If you try to launch F4se with MO and it errors or just shows a black box first verify that it will work by running it from the default game folder. If you have a different fix please feel free to comment! After I had this issue it seems that many other people had the same issue or close with multiple resolutions so I figured I'd make a thread that will sum up all of those.

Mod organizer not working