I'm not sure if this is the proper place for this, so feel free to move it if needed.
I experienced a problem with disabling the always run in the SkyrimPrefs.ini through the Enderal launcher. The launcher didn't seem to recognize the change and kept setting the .ini back to the default (=1 instead of =0).
I solved this by changing the entry in the SkyrimPrefs.ini in the directory itself (C:/Program Files (x86)/Steam/steamapps/common/Skyrim/Skyrim/SkyrimPrefs.ini) rather than through the Enderal launcher.