There are several possible reasons for this. There used to be a bug where a craft that was launched would not always be constructed exactly the same way it was in the vab/sph, but I heard that there are rare cases in which this can still happen. Also, with the way PhysX works, if your computer is having issues keeping a good framerate, then it will round some things, which will sometimes cause parts to be slightly out of place. Maybe your anti-virus was doing something the first time, and slowed down ksp a bit? Or it could just pilot error.