Issues running Skyrim through MO

So I have done all of the steps through getting to mod organizer. I have a non steam version of the game and every time I run SKSE through ModOrganizer (MO) the following occurs:

 - Click Run in MO for SKSE
 - MO closes (I know that's just a setting in MO)
 - What looks like a command console or script program briefly opens and then closes
 - About 30 seconds passes by
 - A smaller black program window appears in the upper left corner and then closes

It looks like a similar startup process to the installation tutorials but instead of the smaller window opening into Skyrim, it just closes and nothing happens. I was able to open the game through the Skyrim Launcher in MO but the game crashed in loading a save (probably because there was no SKSE involved). Any ideas on how I can get this fixed?

Check out my thread about game quitting it might help you