In your "Send to 3D Print Service Dialog" click the option button make sure the export units are what you want. I have a hunch it is set to centimeters.
can you post your exported STL? or have you tried to import the STL back to the software you exported from. It looks like Inventor. When I tried to export from inventor I ran into no problems.
1. made a 1 inch box
2. export the box using Export >> CAD format
3. In the save as Choose STL and then Options
4. Under unis change to Inches if it is not already. The default was centimeters.
5. Import into S3D and the "Auto Scale Option" opened. Clicked yes
and got this.
looks like a 1 inch box.