There are a few factors to think of.
1. Did you vacuum the surface of the material before moving to the next grit. If you miss this step it leaves small amounts of the grit just sanded with and you basically work that grit back into the surface.
2. Inspect your paper and the pad on your sender. Make sure there are not any tears in the edges of the paper and also make sure there are no dings or dents in the edges of your pad. This will cause lots and lots of scratches trust me. A good pad and fresh paper does wonders.
3. Make sure you are not tipping the sander at all or pushing to hard. The sander should float flat and true to the surface. Also, turn your dust extractor all the way to low. You don't need to much vacuum force to extract 99% of the dust made. Having your vacuum on to high will cause scratches.
If you follow these rules you should get a perfect finish. One thing to always remember is the lower the grit you start the more sanding time you will have to do. What I like to do is to have all my friends wood thrown through a wide belt sander or drum sander with 150 grit. Than with my orbital I start at 180 and bypass all other grits. If you start at 100 grit your your Rotex there is a technique to use to ensure and smooth scratch free sand. on your starting grit start in Rotex and get your material to the thickness air evenness you need it to be. Than with the same grit go to eccentric and sand the large Rotex swirls out. Vacuum the material and move forth to your next grit and sand the piece in Rotex. Switch again to eccentric mode after getting the scratch marks our in Rotex mode from the previous grit and continue to your desired grit.
The last thing I consider in my standings is do I need a scratch free finish. 90% of the time I do so I sand all the way to 220 grit not skipping a grit ever. For my furniture pieces 25% of the work is cutting and assembly and 75% sanding. I always remember that sanding is a long tedious process to get a perfect finish. Your Festool sanders just happen to make it 90% more efficient and easier.