I've done what you suggested and after removing Freeflow Florida and UT USA, i was finally able to land and take off on from any runway.
The clears up the problem not being related to our scenery.
That being said, I added Ultimate Terrain back and was able to take off using runway from midways on 9L taking off over the atlantic. Unfortuantely any attempts to take off using runway 27R, the system would crash to desktop. So there is a scenery file that is conflicting with UTUSA that's near Runway 9L/13 as that is the area that causes the crash.
Nothing in our scenery is "causing" a conflict with Ultimate Terrain, it's the other way around: an UT USA scenery file has a problem.
Have you tried running with Freeflow + UT USA only, with KFLL disabled ?