Some MKV files show in my Media server folder but others might not :-(

Ive got my Hub connected to my router and my PC the same. I can access my video folder using Media Server which I drag and drop my downloaded videos (MKV,AVI) on PC. The thing is some will show and a few might not and there the same format so really confused. Whats better to use for Network Share or Media Server? Any help would be really appreciated Thanks

Network Share. They should all show.