Start with the one file.
If that is successful, do another, larger one. Then another one.
By now you have confirmed my suspicion and you can now direct your attention to finding a way to remux those files in “batch mode”.
It might be now possible with mkvtoolnix directly. I seem to remember that the release notes contained something about batch mode.
But even if not, this can be also achieved by using a tiny shell script or batch file.
An example for Windows can be found here: Solution for Audio: Unknown - #6 by OttoKerner
