So why does the viewer automatically disable AA/AF?

Whenever I run SL, it turns off all Anti-Aliasing and Anisotropic Filtering settings I have set in my GPU's driver settings page. Last I checked I should be able to choose between performance and quality myself, not have it forced on me by whatever programs I am running. I literally have to open my drivers settings page, set all the options to minimum, then to where I want them and hit apply, and keep that window open until SL has started, then close it. And do that every time I want to start SL. Convenient.

Sounds like you have your GPU's driver profile set to "application controlled", and/or you don't have AA & AF setup in SL, or a combination of the two. Can't think of any other reason SL could override the drivers settings.