I will have to do some more testing to see if it resolved my main issue though.

This works!

Just to recap so you don't have to read through this rather wordy thread: The PS3 will play back .TS files with the original AC3 audio track from the Freeview|HD broadcast (once the HE-AAC audio streams have been removed) with no trouble and no playback issues. The files that have had the HE-AAC converted to AC3 will not, whatever transcoder you use.

Furthermore if the program was broadcast in DD 5.1 then this will be preserved in the final recording. (In fact it always records 6 channels but only the Left and Right front channels contain any data for non 5.1 programs). 

Not an ideal solution for me as only TV1, 2, and 3 broadcast in AC3 so I think I am just going to put up with it and hope that all the channels will eventually broadcast in AC3, not likely I know.