I am having the same problem and was wondering if anybody figured out what was going on and how to fix it.
I just set up a firefly server on my HPMediaVault NAS, and the ROKU has no problems seeing the media - the only issue seems to be the zero length playlists.
I have tried creating the playlists with WinAmp and WMP 11 (saving as an M3u file) with the same result. The path in the playlist file is using the full network path - \\HPMediaVault\...
Thanks for your help,