Don't seem to have helped much so far, Stew.

You may just have 'lost contact' with ATC - I've done that once or twice, usually by failing to acknowledge a handoff. So the Tower won't 'hand you off' to Ground Control because it doesn't 'know' you're there. The solution (if, like me, you're in the habit of saving flights and then starting again from the same location, time etc.) is to set up a 'new' flight.
As to the time getting scrambled, this often happens in FS9, very possibly it's not the same problem. The only solution to the time-change problem is to make notes at the beginning and end of each flight, and check and if necessary correct the time occasionally while you're in flight. You SHOULD find, though, that it's the date that tends to change, not the actual time. One tip - take a note of Zulu Time (GMT) as well as local time, it could just be that you're crossing into a different timezone. That often happens in Oz, Adelaide is half an hour behind Melbourne and Sydney and Perth is a full two hours back.
Still mystified by the scenery thing. Only thing I can suggest is to delete your FS9.cfg file and let the game build you a new one next time it starts up. Details on how to do that in a thread at the top of FAQ's.