I have had that happen to me on a few occassions with FSX since release. I have never been able to get a handle on a possible cause but I guess it has to do with the fact that it seems a few seconds after a ... mis-calculated landing, the sim starts to reboot the flight, generally back to the start, at the airport and on the runway or parked ready to start over again. It may just be too much information trying to be digested at once.
A really wierd one happened to me recently. I was about 30 minutes out of Seattle heading north in the ultralite. I figure it's time to get the speed up so I pause the sim, hit the alt key and switch to my T-6 Texan. A bit later I see a little uncontrolled grass airstrip sitting in a tight position in a valley, I was feeling up to the challenge and wanted to see if I could bang it into that tight spot. Got it on the ground safely with full flaps and the engine throttled all the way back. I'm thinking on which end of this grass strip has the lowest trees to clear on takeoff. I was feeling pretty accomplished, right up to the point where I over braked and she nosed over. Well, it didn't CTD the sim and when it rebooted it picked up right at the point where I switched from the ultralite to the T-6, in the air. I don't remember ever having that experience before?