II use a few mods, and it seems that every time I start the game I have to go to the Skyrim Launcher and check "load loose files".
does anyone know if there's a way to set this checkbox otherwise? I looked through the various INI files and nothing seemed to do the trick - maybe a command line argument?

This happened with the last game "Oblivion" as well.

It's kind of like checking to see if the refrigerator light stays on when you close the refrigerator door.

What you need to do, is check the files ONCE, then whenever you start the game, STOP clicking on DATA FILES to see if "load loose files" is checked.

Wait for the modding machine to kick in to production drive. That check box won't be necessary.