If I've understood you correctly, you have copied new files to the USB stick, then ran MyDefrag, and after that the new files were gone? Did you check if the new files were really there, before running MyDefrag? MyDefrag only moves files on the volume itself, it does not delete anything. See How safe is MyDefrag?
If the used space of the stick is shown as full, but there are almost no files present, try checking the stick with Windows Checkdisk (you can find it in the properties of the drive).
An other thing may be that these files somehow got a "Hidden" or "System" attribute and the Explorer is (by default) configured to not show these files. You can make the Explorer display these files but it depends on your Windows version how to do that.