Compression issues in Handbrake

[TopWargamer]

So I'm trying to compress down my anime hard drive again (because I finally figured out the proper way to do it without my subtitles getting borked) and some of the video files aren't being compressed.

 

So I'll put a bunch of different video files in Handbrake so that they can be compressed. Some turn out just fine, and others come out to be '0 bytes' once they're done being "compressed." So far I've only noticed this on mkv files, but the other files that turned out just fine were also mkv files.

 

Does anybody know how I can fix this?

 

(As a side note, I am using the latest Handbrake nightly, so that may have something to do with it, but I've tried to compress these certain video files multiple times, and each time it wasn't working...)