It's not a JWPlayer issue, this happens with a regular html5 video tag aswell.
If you take a look at the 1st screenshot (frontend.png) you'll see 2 html5 videos. The top one being the Video library file, the 2nd being a manually uploaded (outside of SF) videofile.
The first doesn't allow for seeking, the second does. Maybe some tools report both mime-types as video/mp4 but if you take a look at the Fiddler screenshot, you immediately spot the problem.
The library video's is served 200 as an octet-stream, the manually referenced one comes back as a 206 with video/mp4. (Also note the size difference, although they are the same video file the '206' is served proportionally).
Since library served files (db or filestorage provider) are served as an octet-stream, seeking will never work.