http://www.bunkus.org/videotools/mkvtoolnix/sources/mkvtoolnix-0.9.6.tar.bz2 It depends on libeblm (http://dl.matroska.org/downloads/libebml/) and libmatroska (http://dl.matroska.org/downloads/libmatroska/) which new versions are also available, that is 0.7.2 and 0.7.4
0.9.7 is out. I'll attend to this bug tonight if no one else beats me to it :)
0.9.7 in cvs. Thank you for reporting.