You should make this post in the MKVToolNix thread here:
https://forum.doom9.org/showthread.php?t=155732
This is the thread for the gMKVExtractGUI application, which only uses the mkvextract.exe as is from the MKVToolNix tools.
You should also always use the latest versions of both MKVToolNix and gMKVExtractGUI, in case you stumbled on a bug that is already solved.