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OK. I believe I have figured out the exact work flow which results in not being able to select a clip. These steps assume no part of the mentioned bus and related connections exist or are configured.

1. Enable the Dedicated MIDI control I/O feature in Options/MIDI. (restart Qtractor if needed... I can't remember).
2. Create a duplex MIDI bus. For the purpose of this thread, we'll name it CCAuto.
3. Create a track assigned to use the CCAuto MIDI output.
4. Create a clip on the new track (can be empty).
5. In Connections , connect Qtractor/CCAuto to Qtractor/Control on the MIDI tab.

The previously created clip (or any clip for that matter) can not be selected by clicking on it.

FIX: The fix is simple; change the previously mentioned track's MIDI output back to master; save; then change it back to the CCAuto.

Any clip can now be selected.