Not sure what version of the addon I was on (Quite an old one I suspect), but I updated it after posting the question to see if that has any impact.
I have no parental controls enabled and there is no apparent pattern to files that are not appearing. Some just don't appear. Usually ones in playlists but I have some of the "raw" source folders exposed too and when they dont appear - they don't appear anywhere.
Don't think its the files themselves either because I have seen some of them listed one day then a few weeks later there they are gone. I realise this isnt very helpful - which is why I was asking if there was a way to help diagnose it

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