Do you habe the newest launcher? Version A49 (it should update itself, but sometimes there are some problems with the write protection)
If I could take a look into your LauncherLog, i could tell you more:
C:\program files(x86)\Steam\steamapps\common\Skyrim\EnderalLauncher\system\log\Launcher.log
Could be a damaged or strange setting in your .ini's because by clicking on settings the launcher tries to get access to them. Try to remove all your .ini's (just save them somewhere). Then let the launcher create new ones.