i am having the same issue on both a wdlive and a wd live plus
ntfs drives
no issue with mkv before the upgrade once i went to 1.06 everytime i pugin the external usb drive all mkv files are set to a zero file size
this is occuring on 2 different wd units and 2 different externals (1 seagate and 1 hitachi)
i properly eject the drives before powering off
file system is fine as per check in windows
There is a bug!! in 1.06