So I set it up so it would start 5 minutes in and encode 15 minutes. What I got was a DCP the length of the full film, with audio starting at the beginning and ending at the end (i.e no trimming), however the video starts from 5 minutes in and goes for 15 mins (i.e. trimming worked). It has done the trimming as asked for image but not audio. This means the audio is massively out of sync, by 5 minutes.
The good new is my audio problem seems to be sorted and it looks great (think the gamma was 2.2).