If you are trying to setup a smooth scrolling article in a folio....
1. Setup the folio for 1024x768
2. As bob sais, put _h at the end of the inDesign docs file name.
3. Make sure that document and it's links are in their own folder.
4. In the folio builder panel, choose import to add the article and choose the folder with the inDesign doc.
5. I have found in the import dialogue box, when choosing smooth scrolling, I have had to choose scroll in both direction, even though it would only scroll in one direction.
This should work, I have done it many times myself, with great success.