Looks like Fluidsynth introduced a 10 ms minimum note length a few years ago. And as LMMS doesn't fetch any audio from Fluidsynth when muted it goes more or less like this: noteon -> noteoff -> fetch audio (much later), which is when that 10 ms note gets played.
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Patch to set minimum note length to 0 ms
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NB. This fix will cause some issues that must be dealt with! Short enough notes will probably go missing.
https://github.com/LMMS/lmms/commit/2dc02001b76e127654660d4a2b2432b7e298d658