I apologise that this isn't a 'proper' answer. (i.e. I can't tell you how to fix your problem with VLC). However,. I hope that it might still help.
I'm a great fan of VLC and I've often recommended it here on AB. However, I still find that there are a few files that VLC occasionally has problems with. I came across a recommendation for the GOM video player, which several people rated as far better than VLC. My own opinion is that it's a case of 'horses for courses'. (i.e. VLC is best for some files, GOM is best for others).
So, you might like to try GOM for viewing your downloaded files. Perhaps it will work where VLC won't? It's a free download, here:
http://gomplayer.com/
Chris