TBH just tested it few seconds ago. I usually play with 60 fps, now i have got 165 fps. I really dont feel any difference. Maybe (It's my opinion though) some shoots which shouldnt hit, hit the opponent.
To Remilia try version 1.1.0.6 and enable the box "Force aggressive API detection "
When starting FL the first time, there is no issue at all. After switching to Desktop and back I had the same issue with the FPS being locked to 60. When making changes in the CCC like for the Catalyst AI and save those changes, Freelancer did run on usual FPS ... until I switched to Desktop and back again.
As suggested here I tried Radeon Pro: worked fine so far (8 out of 10 times when switching to the desktop and back), but unfortunately not every time.
What fixed the issue for me now was deinstalling any ATI related software and graphics drivers and installing latest Omega drivers including ATI tray tools. I'm using a Mobility Radeon HD 2600, so no idea if this will work out with other ATI graphic card models as well.