I don't know if you've found the problem yet, but I have similar issues. Some additional things I've observed that may help with troubleshooting: Files made with MakeMKV also lock. With both MakeMKV and those processed by Handbrake, not including the audio stream allows the file to load. Even with the audio stream, re-muxing Handbrake-encoded files using mkvMerge allows the file to load. This does not work with Make MKV files. Occasionally, editing the re-muxed Handbrake files produces minor to moderate artifacts (a scrambled first keyframe and distorted/missing audio appx 15 seconds before the point where the file was cut. The artifacts only occur with files where Handbrake did not automatically recognize and include the audio, forcing me to manually add the track.
I've only tested this on 64-bit Win 7.
Hope this helps.