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I'm attaching a screenshot which shows plugins and configuration. The "bass" track is using qmidiarp and yoshimi. The midi track is just playing long base notes that are modified by qmidiarp.
http://picpaste.com/qtractor_qmidiarp-5HjJ4OPq.jpg

re missing first note: I understand that it could be a qmidiarp problem as well. qmidiarp is built from source (trunk) about one week ago, so it is the latest copy. I am using qtractor 0.8.1 from kxstudio on Ubuntu 17.04.