Problem with multiplexing two mp4 files

I have an mp4 file that I have upscaled to 2K, creating another mp4 file. Both versions play correctly. I want to join the audio track of the first and the video track of the latter, unto an mkv file. Problem is, no matter how I try to multiplex, I get an unplayable mkv file showing a length of 2:26:44 instead of the original 1:11:44. I believe this is due a bug in mkvtoolsnix.