I installed Lubuntu 12.04 and followed the PrepareForUbuntuStudio on the Ubuntu site.
I start qjackctl (0.3.9), qsynth and qtractor (0.5.5). Then I start the qjackctl (start-button).
I play some songs (works fine) and then I stop qtractor and qsynth.
When I klick the Stop-button I get an error message that there are some still running.
Do you have any clue?