If the file plays fine without subtitles selected, the problem is the sub and just because it was multiplexed into the container does not mean the sub was made properly. The most usual condition is that the FPS is missing from the sub. While this will most generally play in other players because most of them are taking the frame rate of the video and applying it to the sub but this is against the specifications of most all of the subtitle formats and does not negate the fact that the real problem here is the subtitle. When the subtitle file is incorrect for the video or the FPS specification is missing the problems will range from simple drift in time to causing the video not to play.
VLC supports some 9 different Subtitle formats, but is does not support positional information, color or embedded fonts available in a few of them. This is being considered for the next revision.