Under [Main], set SaveSettings to 1 and adjust all your settings to how you like it, load the game and exit, then change SaveSettings back to 0. This prevents the INI from being written to because of the FrameRate Manager. It adjusts settings on the fly and exiting the game can save those settings in mid-change.
Just keep in mind if you want to change settings in-game, you need to set SaveSettings to 1 first. Or change them via the Oblivion.ini and a text editor outside of the game.