Pedal C on a flugel horn pops out so nicely, because unlike on a trumpet it is an actual note. On a cylindrical bore trumpet, the overtones are too far apart and the first interval is fairly close to the Clarinet's 12th than the octave we desire. The flaring bell fixes things fairly well for the higher overtones, but that first interval is just plain too wide. So we tune the trumpet so that the low C is in tune and leave the Pedal around a minor third flat. The supposed "Pedal C" of a trumpet is actually an artifical one, a 2nd order effect supported by the fact that some of the overtones of this pitch you wish to play DO match up with resonances of the instrument - namely low C and G.
On a conical bore flugel, Pedal C is a real in-tune note. But this seems to have an unintended consequence for the production of the artifical notes in the F#-C range. I'm guessing that the presence of a strong resonance at pedal C means there is a stronger anti-resonance in the F#-C range than on a trumpet where they pedal resonance is flat, out of the way and probably weaker. So this anti-resonance interferes with your ability to play these notes with minimal 2nd-order support from higher resonances.
Long live the 4 valve flugel (actually, I've often thought it would be interesting to have a fully compensating 4 - valve instrument that would basically be both a flugel and an alto horn in F)
Christopher C. Stratton
Engineer, Hornist, and Brass Instrument Maker