The difference is between the definition itself.
Free Flight : Free flight is a developing air traffic control method that uses no centralized control (e.g. air traffic controllers). Instead, parts of airspace are reserved dynamically and automatically in a distributed way using computer communication to ensure the required separation between aircraft. This new system may be implemented into the U.S. air traffic control system in the next decade. Its potential impact on the operations of the national airspace system is disputed, however.
This effectively means that, if a part of space is reserved for free flight, you can effectively do anything with your flight plan. Moreover this reserved space would change dynamically, so if there is an approaching aircraft nearby., your free flight space changes to accommodate free flight space for the other flight as well. Both of the planes would have DIFFERENT free flight space, and they can adjust their flight plan just in their own flight space. This eliminates the need for ATC completely.
Free Route Airspace : Free Route Airspace (FRA) is a specified airspace within which users may freely plan a route between a defined entry point and a defined exit point. Subject to airspace availability, the route can be planned directly from one to the other or via intermediate (published or unpublished) way points, without reference to the ATS route network. Within this airspace, flights remain subject to air traffic control.
Here, the Airspace allotment remains under the control of the ATC, which allocates single space to multiple planes, and there one can decide which path to take. Here, inherently there is a possibility of overlapping routes (Because of the same airspace being allotted to multiple planes), and thats why, some routes are allowed in this space, and some are not.