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i really can't see how all this happens.

but you can try a few shots in the dark, one by one, exclusive and/or inclusive:

1. update from latest svn trunk.
2. build for debug (./configure --enable-debug), start from a terminal console and watch for the verbose output.
3. enable dedicated MIDI control ports but don't connect them at this time (View/Options.../MIDI/Dedicated MIDI control input/output = On).
4. disable all MIDI transport/sync master/slave related options (View/Options.../MIDI/MMC = None, SPP = None, Clock = None).
5. disable all JACK transport/sync master/slave related options (View/Options.../Audio/Transport mode = None).
6. move all the clips away from absolute 0 location eg. move all of them to beginning of bar 2; reset loop points accordingly.
7. remove any MIDI connections (yes, you won't hear any sound but this is for testing purposes right?).

please, test && tell
cheers