1 Format device
2 Do Auto-sync
3 Inspect device node in tree
Duplicate files are seen.
Then to prove these are definitely distinct files:
4 On device, play one duplicate once, the other twice
5 Inspect in tree
Different Played # is seen.
e.g. see

In this case, three out of 247 files were duplicated. The number varies.
EDIT: info from a another instance can be found here http://www.mediamonkey.com/forum/viewto ... 76#p172376 .
Tracked at http://www.ventismedia.com/mantis/view.php?id=5864