I have some small MP4 Files i wanna remux to MKV, around 3,5 minutes and 100MB. After muxing the file is 200 MB and 7 Minutes. Last half without audio. File muxes fine until mkvtoolnix-64bit-9.9.0, but not with mkvtoolnix-64bit-11.0.0 and after. (Also tested 14.x, 16.x and 19.x i had layin' around, all have the same problem). GUI or CMDline delivers same result. I'm on Win 10. I did not encode the MP4s, so there is definitely a possibility that the MP4s are guilty, but then its weird that 9.x just works fine.

Link to Testfile: http://www.share-online.biz/dl/2JWKSH2PVL9