Aere, thank you for reporting this issue. I'd be willing to test this out but I actually have a deadline soon for some music I need to compose with FluidSynth. I can't have FluidSynth break in the next few weeks. Therefore, I'm very glad you warned me and I'll hold off upgrading to 11.10 until I finish this music.
After that (in about two weeks), I'll do the upgrade and then report back with my findings.
One thing to try though: you say you're using JACK. I've had serious problems with JACK in the past and decided it wasn't worth it. For years, I've just been using FluidSynth with ALSA and/or PulseAudio (it doesn't make much difference to me). So you might try those and see if they work for you.
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