I had exactly the same issue: although Harmy’s mkv files play fine in VLC, I can’t get NJVC’s iso files to play the main movie in VLC. (All of his extras seem to work, however.)
Fortunately, my stand-alone Bluray player worked fine with the iso files burned to BR-DL discs. Well, nearly fine… It didn’t like the default audio track for some reason. The picture was a little jerky (looked like a frame skip about once every second or two) until I tried another audio track at which point all was fine.