As discussed on the Tools page, MKVtools is an Objective-C application that acts as an interface for a number of UNIX commandline applications. So if you encounter problems with MKVtools, chances are that it's an issue with one of the UNIX applications.
To help evaluate causes of strange behavior, you can select to keep the log files that are created during processing. This option is found in the MKVtools preferences . Examining these log files should give you some hints regarding what the Unix applications are having issues with. The web sites for the individual Tools could also prove helpful.
Probably the best resource would be useful Mac video forums found here or here. You'll find lots of people there willing to help and with more knowledge about general video issues than I have. Also, I periodically read this forum and can chime in with specific MKVtools issues.
- None at this time.
- The output video is missing, smaller than it should be, or is not playable: Some error occurred during processing. Check the log file(s) that should have been created (if keep log files is checked in preferences) for error messages.
- Joined videos are not playing properly: Joining can be hit or miss. Usually it requires a complete re-encode like what quicktime does, but often we can get around that, which is what MKVtools tries to do. Success mostly depends on how the originals were encoded. There are some tweaks that you can try when you don't get good results. Joining just a few files at a time can be successful. Processing the files through MKVtools first (passthru or you might have to re-encode some of the tracks) can also improve results.