Has the usb disk partition been given the label "hd" at some point in its history, as that would explain why it was mounting in a folder named /media/hd.
If any usb disks I own are not already labeled appropriately by their manufacturer, I quickly give them a label I will know and recognise to make life that little bit easier for me.
Odd about those two folders that will not copy, however. Must be a permissions problem of some sort, I suspect.
Xubuntu 12.04 user, and loving it!