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Ardour's playback is aligned to master-out: "When the playback clock reads 01:00:00:00, the sample corresponding to 01:00:00:00 is audible at the speaker(s)" When exporting, and grabbing data from output ports, the signal is offset by the master-bus physical playback latency. This was compensated for, but lead to initial silence in the exported file. New approach is to start capturing export data during pre-roll, at the time when playback is written to the output buffers. To also shaves off a common offset to make this work with realtime export. Effectively this emulates processing with disconnected master-output port, while still keeping any latency of effects on the master-bus itself. Last but not least: jack updates latencies when freewheeling, (setting HW latency to zero). The callback arrives asynchronously some time after enabling freewheeling, but after Export Ports have been configured. Those callbacks are ignored.
Please see the Ardour web site at http://ardour.org/ for all documentation..
For information on building ardour:
http://ardour.org/development.html