Egh & Palikrovol: Can you please test whether or not this happens with older versions of mkvtoolnix, too? I'm especially interested in 2.9.7 (release) and earlier test builds of 2.9.8 (164 or earlier). Here are direct links to both versions:
http://www.bunkus.org/videotools/mkv....9.7-setup.exe
http://www.bunkus.org/videotools/mkv...-164-setup.exe
Please always make sure that you save the .mmg file and load it with the same version, e.g. don't try to load a .mmg with 2.9.7 that was saved with 2.9.8-174.
Thanks for the feedback.