Reduce Transparency Keeps Turning Itself Off
The symptoms you describe are likely caused by the preference not getting saved to disk. This is caused by a problem with the file permissions, or if the preference file somehow got corrupted.

If this is the case, you can move the preference file (I think the relevant one is ~/Library/Preferences/com.apple.universalaccess.plist) from its location: this will cause the preference file to be recreated.

Of course this will work also for other preferences (though identifying the correct file isn't always as easy); remember to keep the file around (instead of deleting it) so you can restore it in case this fix doesn't work.