Understood. I perceive your goal is to get it to play correctly in Media Center. If so, it is helpful to understand what is tripping up MC. First you want to rule out issues with the file. That VLC plays it may indicate it is more forgiving in this case, not that the file has no internal errors.
There may be other things that will resolve the matter, but eliminating obvious problems is the first step.
Would you be willing to upload the file (in private) so that I can test it? If so, use one of the various large file upload sites.
