Greetings, I am having the same problem. Skyrim runs fine through it's launcher. However, when running Skyrim or SKSE through mod organizer, it simply shows the Dragon logo with fog behind it. No menu appears no matter how long you wait. It seems that this is a problem that has affected only a small amount of people so no solution has been found. All the same, its rather annoying. OP and I could sue some help.