The software (all versions and titles) are programmed to align walls based upon the "main" or structural layer (the layer that bares the structural loading of a wall). So when the floors of two or more floors do not by default align, it is your job to manually align them wall by wall, floor to floor.
The makers of the software have done a great job of this in MOST applications but where the walls do not naturally align, it is your job to make them aligned.
DJP