I guess you need to unlock the full version purchse. Open the settings tab, select In App Purchases and then tap on "Restore Purchases". You need to do that whenever you reinstall the app. After this step, refresh the songlist again and all remaining songs will be added.
NeilC I have noticed there are a few M4a files in this file share as I drag and dropped a lot of my backing tracks
Will ST3 still recognize them and will iPad play them as they ain’t MP3 ?
These are the files you imported through iTunes. As I wrote above ST3 needs to transcode these iTunes files and stores them as m4a files. ST3 can play multiple file formats. So it does not really care if a file is mp3 or m4a. But keep in mind, if you have a mp3 version and a m4a version of a song, it will be displayed as 2 identical songs in ST3. You will only see a difference in the song details (different filename).