I have a similar issue, every time I start S3D, the FFF process is completely gone. If I click ADD to add a new process, it usually adds the process with the same settings as I was previously using but not always. This is another example how tight security prevents the registry from being properly updated with the new process/profile settings. I really wish the settings were moved from registry storage to file storage. The registry, in my opinion, is not the place to store these settings, for one, the amount of data can become extremely large if you create multiple setting profiles and that just consumes way too much memory. The larger the registry, the slower the computer becomes. Secondly, it is much safer to examine and backup a text or xml file than going into the registry and since there is no confirmation of making a change within the registry, it is very easy to accidentally hit a key without knowing you hit it which then saves that wrong value when you exit regedit automatically without your knowledge.
Please consider changing the way profiles are stored and organized. This is one of my biggest pet peeves of this software. In order to have profiles that include ALL settings from the FFF settings window, we have been directed to add entries for the settings you want to preserve that are currently not automatically saved.
It show's to go you how feelish you fool when your tang is all tungled up and you bart stalking tackwards!