http://sourceforge.net/projects/mkvextractgui-2/You're using an old version of mkvextractgui, which likely has issues with more recent mkvtoolnix builds, try updating to mkvextractgui-2 and see if that does it.
Also, in order to remux from mkv to mp4, demuxing first should be unnecessary. Assuming you have yamb, just load the mkv itself and see if it works (it should).