Final Edit (hopefully):
I had a problem with dts files not being recognized by AudioMuxer.
By testing and testing I discovered that sometimes when trying to feed to Audiomuxer some dts files, mediainfo.exe crashed and locked the program. I went into the roaming data directory and discovered that the mediainfo version used is an old one. It's 0.7.61, dating back to October 22nd 2012. I downloaded the CLI version from here (https://mediaarea.net/download/binary/mediainfo/0.7.91/MediaInfo_CLI_0.7.91_Windows_i386.zip), which is just an exe file with no external DLL. I renamed the mediainfo.exe to a .bak version and copied the new version over in the C:\Users\gorman\AppData\Roaming\AudioMuxer\MediaInfo directory.
And all the files are working just fine. I advise to update the mediainfo version you use in the installer. Four years is a long time in this world.
Hope you'll find my journey useful. I spent long hours in solving this.