It's not a bit deal since I invariably end up modifying the headers or entirely remuxing the files but its a few extra clicks I'd sooner not have to do.
I found the following but that doesn't seem to apply to the Windows version:
https://www.makemkv.com/forum2/viewtopic.php?f=4&t=7505
Note: I want the subtitle files to be included with the file, so its not a matter of stripping them out, I just don't want them being marked as default since 95% of the time time I don't need them there front and centre
