Hi,
Couple of years on… similar issue.
Have been Experimenting with Independent track loop this evening and have a very similar behaviour to what you described above.
I tested with an empty project.
2 Instances of Halion 6
1 Audio loop from media bay
I found the following issues.
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Timeline on key editor out of sync with timeline on project window.
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Turning on independent track loop in instance 1 of hal6 turned it on for instance 2.
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Every time I clicked on a different track and then back to a midi part, the track loop would still be on and working but the loop markers would have defaulted back to 0 on the time line. So still working but potentially confusing.
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Turned it on in the audio part, clicked to a different track and back to the audio part; and the independent track loop has turned off and is not working at all.
In this current state I find this tool completely unusable. I think this is a real shame as its quite a simple idea and would be really handy for sketching down ideas. I realise I can duplicate midi and audio parts but this way seems far more fun and efficient. It would definitely add to my workflow when writing tunes.