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Hi Craig,
Sorry its taken a while to get back to this, I have been looking into a few working theories and the latest that seems to have some weight to it is the folder depth the rasters are stored in.Too deep and the server won't read it hence using the staging folder. Some of our users have also commented that in some cases arcgis server doesnt seem to register all the subfolders in a registered folder. I haven't had a chance to test this but will post back when I have.
Dave