how much different? Same as if they were not scaled? I can not say I have ever done this, but sounds odd.
I would scale the part and note the scaling sizes, print the part and make sure it is correct. Then remove the model from s3d, import it, duplicate it and scale them all at the same time. Then move them around where you want them.
Oh and another thing that could be happening is, and I can not remember the keys as I do this accidentally.. I think it is control wheel.. it will scale the part. I do this sometimes by accident when moving stuff around.. If this happens control-z is your friend. Don't have S3d on the computer I am currently using or I would verify the key/mouse combo that does this..