I have tried to replicate the problem but was not able to – in spite of your very accurate explanation. What you are observing is that the Notes do not get generated correctly, right? So that is really independent of the synth you are using in the "back-end".
I have both listened to a mono synth and monitored the MIDI stream, but do not see any irregularities. I have tried three notes on different tracks, different pitches and all possible permutations of length combinations, especially overlaps.
Has anyone else been able to re-produce this?
It seems rather strange that something this basic would have passed unnoticed for such a long time now.
Another question to you would be how your MIDI stream is routed – do you go via direct wires, or do you have any other devices between Octopus and the Synth or the MIDI interface that is providing the measurement? Possibly the messages get produced but filtered somewhere in between?