Are you sure that they are all the same?
I would download and install G-Spot, and put one of the "good ones" into it, then put one of the"bad ones" into the program. Do a screen-cap of the G-Spot screen with a bad file, and we can tell you what is different, and what is wrong.
Also, see this ARTICLE on what can be inside most popular file formats, which are but wrappers.
Note: there is a link to G-Spot and to MediaInfo in that article.