I have exactly the same problem:
"While in flight and on autopilot, if I go to make a change weather it be in views, options, aircraft or any of the choices, and then hit OK and go back to my flight, all my intial navigation input, lighting, auto pilot settings etc..have all gone away."
It started after I downloaded 1.3 and added the BOAC 300C. Prior to that, no issue. I have made no config changes nor have downloded anyother thing to my FSX and CS 707.
Any Ideas?

Kirt