The version of your DDR depends on with what FileMaker feature you generated the DDR with.
If you used the feature Tools -> Database Design Report... then your FMVersion solution should be marked as "Using the Database Design Report".
If your DDR was generated using Tools -> Save a Copy as XML or the Save a Copy as XML your FMVersion solution should be marked as "Using Save a copy as XML".
The difference between these Solution types is not only the format of the DDR, but with FileMakers new "Save a copy" as XML feature, you are also able to use our API to push your new DDR to FMVersion and start a comparison with just a click of a button.
FileMaker Tools Menu FMVersion DDR Options