Options in the main menu only apply for historical missions.
For the campaign, you need to set the gameplay menu options when you are in the bunker before starting your next patrol, you cannot change them during patrol.
This is very important because if you didn't do so before then the gameplay options will default to around 30% only, not necessarily doing what you want.
Just before you start on patrol in the bunker, go in these options and: For high realistic play, set everything enabled except the 'disable external camera' and play with Real Navigation. For less realistic play, you can play without Real Navigation and also disable Manual TDC and other boxes (like the one you mention). Once set, these will also remain in effect for your next patrols until you change them again, but they must be set again if you start a new career or main campaign chapter.
Because one cannot change them when on patrol, I use to always visit these options just before I leave bunker, so I'm sure all is OK
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