When you apply scales and other operations they get put on a stack. Before exporting you need to freeze the transforms. Presuming you're using the mod tool:

Left click the "Transform" header on the right and select "Freeze All Transforms". That'll freeze any scaling/rotation/etc. You'll notice the numbers in the transform box become 1s, since the scale operation has been applied to the model's vertices now.

Click on the "Modeling" and "Object" buttons under the "Freeze History" section on the right. These freeze other things like the texture operator stack and the weight painting stack.

I have a question, how do you import models into XSI? I have downloaded XSI, but I have no idea how to import the models. I am trying to change the size of the ships, especially the capital ships. I am new to this, so I really would appreciate the help.