Did you find the cause of the performance hit from the FDM? The version in Git shows around 110 total/ms.
I seem to have something similar on the 744 now. Altough about half as bad (ca. 400 total/ms) as in your screenshot, it's spending much more time on flight compared to the P51D for example. The P51D also has a big/complex FDM, so it looks like it's not (just) the size/complexity of our FDMs. Maybe a certain JSBSim function that both our aircraft use is troublesome?
EDIT; I've reverted the FDM to the version that was shipped with 2.4, back in 2012. Surprisingly the system monitor value is pretty much the same
Makes me wonder if the monitor groups other things under "flight"...
EDIT2: Apparently not. When I launch the 744 with the UFO fdm, it's down to just 4 total/ms.