When you click the options button for 0SEx you get the option under the "PS" section to choose Keep pvt2 (PCI/DSI) Nav Packs AND Keep Padding Streams.

I don't know what these both mean but when I checked them both off and then used ffmpeg for conversion I got my first ever insync output without having to play around with muxing after the fact.

Was I just lucky or do these options have significance for syncing ?

-Squeed
http://www.squeeds.com
VCD and SVCD Support for MAC