So I did "FIND" in my respective path.
Problem found and almost solved … As I use AFP on my NAS it creates .AppleDouble folders in every folder (on NAS) filled with files with exact same name as original files. When I am trying to add a folder to playlist it adds only files from .AppleDouble directories not original ones.
I was fighting with that issue some time ago when I was trying to use PLEX Server on my Netgear ReadyNas. I completely forgot about .AppleDouble issue. The problem came back after OSX Mavericks upgrade for sure. As my playlist on Dreambox was generated when everything was fine, upgrade to Mavericks didn't change anything in playing my old playlist, but when I decided to move from OE1.6 to 0E2.0 I had to add directories to my playlist once again, but this time with new .AppleDouble folders.
Thanks for your time and patience.