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If you go straight to the files section and not to a user's files via the profile, are the files shown in the list ("All files" for example)? Could any 3rd party plugin be responsible for the issue, i.e. have you disabled non-bundled plugins to see if this solves the issue?
Another possibility is that you may be uploading the files in groups. As the container_guids are different, they wont appear in user profiles
Actually all the files have been uploaded to groups. Is there a way to link files from groups to user profiles? Thanks for all the feedback guys! All help has been much appreciated.