Using the version of Firefly bundled with the Acer HomeStore WHS I moved my iTunes collection over to the WHS and watched as Firefly scanned everything. To my dismay, all tracks appeared twice.
I tried many things, and got no where, so finally upped the debug level to max and looked through the log. The solution ?
I have always placed the iTunes database in a directory located within the iTunes music store. What was happening was that the scan was picking up not only the music files from the iTunes directory, but it was also reading the XML file where iTunes stores the catalogue.
Solution was to rebuild the iTunes database on the WHS and ensure that it was no longer in the iTunes music directories.