Ok, it seems a little contradictory to me to run with filtering and flux anti-aliasing. I would just use anti-aliasing as that will probably be more accurate and doesn’t require empirical tuning. Also from your ini file, the anti-aliasing quad-deg is set to 7 for an order 4 simulation. I don’t think this is high enough for the various solution point layouts, although you’d need to check the quadrature directory in PyFR. See this post Error associated with time step - #6 by p.vincent
Did you try running with anti-aliasing and globally adaptive time stepping?