In answer to your second question, the FAQ has this to say:
The fact that you cannot make global font and ruler changes in Edit Scrivenings is due to the same problem. You are selecting “non-existing” characters when you press Cmd-A.
As for your first question, a number of things could be happening here. It is good to remember that the style defaults in Preferences>Text Editing are just base ruler set ups, and that messing with the ruler after you create the file will change those. Unlike some applications, Scrivener is a full rich text editor, and gives you total control over the look of each document. This gives you flexibility, but also means that you lose uniformity unless you yourself are rigourous in keeping it. The application will not be strict about it.
There is one menu command that you will find interesting: Documents>Convert>Convert to default…
This will reset the selected documents (you can do a bunch at once using the Binder), back to your preferences. Use with care, as if you have special formatting set up, it will blow all of that away.
I’m moving this topic to Tech Support and re-naming it so future users can find it easier.