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Ok, I set it to Fusion.
I have never used the "native desktop environment dialogs" box.

What I notice, is that the audio and midi connections are disconnected when I save a preset. (But I can still use the GUI and change presets.)

This is what QJackCtl reads when it disconnects:

Fri Sep 8 17:14:50 2017: Disconnecting 'a2j:MOTIF8 [24] (capture): MOTIF8 MIDI 1' from 'padthv1:in'
Fri Sep 8 17:14:50 2017: Disconnecting 'padthv1:out_1' from 'system:playback_1'
Fri Sep 8 17:14:50 2017: Disconnecting 'padthv1:out_2' from 'system:playback_2'
17:15:37.200 JACK connection change.
Fri Sep 8 17:15:37 2017: ERROR: Cannot connect ports owned by inactive clients: "padthv1" is not active
Fri Sep 8 17:15:37 2017: ERROR: Cannot connect ports owned by inactive clients: "padthv1" is not active
17:15:41.805 JACK connection change.
Fri Sep 8 17:15:41 2017: ERROR: Cannot connect ports owned by inactive clients: "padthv1" is not active

Hth...

brian