When exporting the setup as LSCP to file the Channel Routing isn't saved. When re-loaded channels are assigned to the default 0/1 for left/right despite being set to e.g. 2/3 previous the export.
Fantasia doesn't recognize the SET CHANNEL AUDIO_OUTPUT_CHANNEL command in hand written LSCP files either when they are run.
Should be fixed now (in the latest CVS version). Thanks for the report.