I remember finding out how to stop it from happening but after I uninstalled skyrim and reinstalled it I cant seem to find the information. I know its only a small tweak, anybody mind cluing me in?

Cheers

Make it read only

You know, the game is supposed to be able to change the INI as it needs to, for mods and such. You do not even get a complete INI file until you launch the game for the first time.

The only sure way is to SKSE or another third party launcher and bypass the official launcher.