Is anyone having any issues with Handbrake not fully encoding MKVs? I ripped a copy of my Lincoln blu-ray and loaded into Handbrake. It chugs right along but the completed file is only about 300MB and the movie is only about 17 minutes of footage.
I've seen some Blu-Rays with multiple "versions" of the movie, some either artificially shortened or in mixed-up order specifically to screw up ripping. That's first thing I'd check; see if there is a track that is reported as slightly shorter than the one you were ripping - that might be the "Real" movie.