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that is exactly the way qsynth/fluidsynth works, you're not doing anything wrong.

many soundfonts are multi-timbral, that meaning that those provide several instrument patches or presets to select from. when first time loading those soundfonts instrument presets are often spread in program number order, one by one, to each of 16 MIDI channels. after that you can edit, select and assign a different preset onto any other channel, if you're not happy with the so called "factory" preset layout.

now, if you load more than one soundfont onto the same engine, you'll have multiple presets that might overlap each other, depending on soundfont's default bank and program numbers. that's why you'll have to plan the stacking order and for bank-offsets when loading more than one soundfont on a same engine, so that you get all or most desired presets as accessible and addressable on the channels assignment list.

hth.
cheers