As described in the Bugreport for 0.8.x I got the same trouble here with 0.9.pre1 : If i have a Segment, that has no Notes at its end, everything works OK but if I stop transport as a note with Vam is played, this very last note is played until i close the App or Mute the whole Instrument in its Metatrack (to mute the Miditrack only does nothing... ,"Reset Instruments" helps also sometimes yet not often).
It is the same with deiconce but not with Zynaddsubfx.
What can this be??
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Well well, looks like I have to apologize - after hacking xorg.conf this bug is gone as well, though i do not see any connection between GUI-stuff and MIDI-issues.
Now the Muse looks and sings just great :-)
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Hmm, not sure how that could influence things either, good that it works though, I'll close it.