I just did a fresh install of Oblivion using the following:

- Oblivion
- NotN expansion
- Shivering Isles
- Unofficial patches
- All official mods (horse armor, orrery, mehrunes razor etc)
- Oscuro's Oblivion Overhaul ver 1.3, 1.31, 1.32, 1.33 and 1.34 beta

What is happening is the video settings and mouse settings do not get saved if exiting the game and reloading. Specifically, the mouse axis (I always reverse), blood decals, water reflections and ripples. I don't touch the other settings, but no doubt they wouldn't be saved if I did. I have to change them every time I start a saved game.

Is there an ini settings that keeps these settings? What could be happening?

Set the settings to what you want them and then open the console up and type in "saveini" without quotes.