You should be able to set any "settings" option with the -o switch. Example:
fluidsynth -o player.reset-synth=0
That should work, if in fact there is a "real reason" why these files are all piano-sounding (i.e., there's something weird about the midi files that's causing them to be reset).
But as I said in my last mail, I experienced this same problem for all MIDI files (for certain combinations of parameters) and it wasn't caused by any settings or whatnot, just a race condition, and it's fixed in Fluidsynth 1.1.2. Try the latest version as a first resort, I'd say.