The problem with many (most?) file formats is that there isn't always a difinitive specification to reference. And even when there is, there are often due facto exceptions or changes to the format later that aren't documented. I seem to recall reading more than one blog post by the developer of Virtual Dub where he was complaining about nonstandard avi files. It seems to be a common occurrence where someone creates a software tool for creating or modifying avi files that does something that's not 100% following the specification. Then the problem is made worse when people who create playback apps code them such that they will silently tolerate non-compliant files. Before you know it, non-compliant files are everywhere. Though, if windows media player can still decipher and play them, are they invalid?
Container formats like mkv are particularly hard to check. Not only would you need to verifiy that the container "envelope" is correct, you'd have to have some way to verify the integrity of each old the audio and video streams contained within, which can be in a multitude of different formats/codecs/bitrates/bit-depths/resolutions/etc...
GroovyMAME support forum on BYOAC
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Re: Bulk file integrity checker for a variety of formats
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