all good i will test what you said and post back their
I see you use Comskip in your signature, does that work well with DVB-S Freeview?
This was discussed on page 312 (I think). Let me guess it is your TV3 recordings you can encode and none of the other channels. That's due to TV3 including an AC3 audio track. The others solely use AAC+ in a LATM container and there isn't any freely available demultiplexer which can handle LATM yet.