Love to help if we can

We need to know a lot more to figure out whats happening.
Your scanner?
What is it scanning as? What type of output does it produce? It could be anything from TIF to PDF and it might have built in a silly paper size (such as "letter") which can distort it when viewing in some other program
Where have you stored the output file?
What do you open the output file with?
Have you seen the "not the same problem on the screen? or printed out?
Sorry to get into the detail, but that is where its going wahoonie-shaped
What is the problem that you are noticing? is it size, or distortion?
Would pictures illustrate the problem - ? a photo of the original and a photo of the scan?
happy to help if we can
andrew