I am working with Revit on a revit server,
i have the same problem with ducuflow as written above. Since i am the only one in my company with that issue, were are out of ideas. 

The export and PDF print settings such as Quality and Raster/Vector and the filename-settings are resetting itself every time I open revit the next day.
the version i am currently using is: 6.5.0.0

I am really looking forward to a solution.

Please upgrade to version 6.2.

To give you a more specific answer we sould need to know what kind of project you are working with: local, workshared on a network drive, BIM360, Revit Server, Autodesk docs, etc.

In any case, a general rule for saving the settings of the advanced filename is that the new Revit project must a named file (saved at least once). 

We recomend that you please use Docuflow 6.0 as a few changes were made for the settings mechanism in the last versions of 5.xx.

Please let us know if you still experience any troubles so we can assist you further.