I'm seeing the same issue with an added, very strange, additional bug. If I advance time warp above 1X and then return to time warp = 1X, most of the ship goes zooming off except for one small section (in one ship, that's orbiting Mun the only part left is a landing can; in the other ship that's orbiting Duna, the only part left is a rover that had been stored in a service large service bay). If I speed up time warp above 1X, the whole ship appears to be intact but if I then slow the time warp back to 1X the majority of the ship goes zooming off again. If I wait while a minute or less (for the ship that's orbiting Mun) then I'll see the rest of the ship zoom past again as though it's continuing to orbit Mun while the Landing Can is appears to be stationary. {I see that other's have reported a similar situation in the bug reports linked above) At time time I created these saves I was using MechJeb, Chatterer, and Kerbal Alarm Clock.