yesterday i had 2 mkv files to join/append. i started the process and nothing happened. i closed mkvmerge gui to restart it. after this the program won't start again. i get a runtime error saying that the application has requested the runtime to terminate it in an unusual way. i did a bit of searching the webs and found a few suggestions (taking ownership of the root drive, the user directory, the personal directory, uninstalling the program and deleting registry entries and reinstalling) to no avail, still won't start. i'm running windows 8.1 if that makes a difference. i decided to just use the command line, but since the documentation was zero help. can't find any alternatives to mux/merge x264/dts/sup/ac3/etc etc, and since i'm converting hundreds of my blurays to mkv for server storage, this is now the limiting step. so before i either format and reinstall my OS (which i just did a month ago) or put a bullet in my brain, please help. thanks.
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(late reply but may be relevant for others)
Have been using MkvToolNix-gui.exe and having problems with it refusing to restart again sometimes after either crashing or just being closed. Happens with portable versions 8.3.0 and 8.5.1 running under Win XP.
In my case, discovered the problem is a semaphore file the program creates and does not remove sometimes when terminated gracefully, and probably always when it crashes. When the program tries to start and finds that legacy semaphore file, it just exits if not already running (if already running it justs pops up the already running instance - can only run a single instance).
In my case under WinXP the file is:
"C:\Documents and Settings\jugulator\Local Settings\Temp\MKVToolNix-GUI-Instance-Communicator.lock"
(location will be different for newer Window versions)
Just delete that lock file, and MKVToolNix-GUI.exe will run again if this is also your problem.