In the last few days I've been getting the black screen then CTD, this was happening in various parts of the world plus on different aircraft and around 1hour in to flight.
After a bit of searching I think I may have cured it, what I did was delete all the scenery.dat files from every scenery file and also deleted the FS9.cfg file. I restarted the sim and it builds new scenery dat files plus a new FS9.cfg I then tried it on a flight and it seemed OK, then before I went to bed last night I set the sim on a trans Atlantic flight to run overnight. I looked this morning and it was still running nicely.
I also did a registry check too, luckily I had a reg cleaner installed but never used it till now, it found a lot of errors and cleaned them in seconds, I think that helped too.
Forgot to add, When I started FS in the past the openening screen was always in the top left corner of the monitor, after I did the clean out above it now is in the centre again.