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I know this is an old thread, but I got a similar problem but the solution was to update the libzen library, needed for mediainfo. I tested the mediainfo cli in the problematic files and realized that > 2gb files in a NTFS external volume in a 32bit Linux were the problem, mediainfo was simply giving no output at all for those files. Check https://sourceforge.net/p/mediainfo/bugs/1077/?limit=25 and related links for more information since it's where I found the solution of upgrading libzen. Probably compiling a newer version of mediainfo would work as well.

@mlaggner if possible, as a suggestion, check if the java code can check for mediainfo empty response somehow (I don't know if that's possible).