The Processing Properties relate to fixes which have to be made or not, and to the information that you would like to see in the preflight report. For example, you can choose to log fixes and include the following information pages in the preflight report:
Furthermore, you can enable or disable all fixes in the Preflight Profile. Indeed, an Enfocus Preflight Profile can do more than just a preflight check of PDF documents: it can also fix detected problems. You can, however, also create a Preflight Profile in which you specify a number of fixes and disable these fixes. You may want to do this if you just want to check PDF documents but not change them now, maybe later.