Not everyone has the same plugins/addons; all it takes is a bad one, or a badly configured one. It's not a global issue as only a few users see it, and apparently only in Firefox, so it's not something MC is doing (if so, it would affect everyone and all browsers).
Firefox automatically renames some files after download - I can see many people on the internets asking about problems caused by this "feature". You can also tell Firefox what to do with each file type after downloading. So what I think happens here, is that JRiver sends the license file tagged as Application/Executable (MIME type) and if the users happens to tell Firefox to "always run" the MJR after download, Firefox helpfully learns that Executables are now called "mjr" files. So it starts renaming any download tagged as Executable. This is why I asked about the MIME type, which is the only thing MC could change to avoid this issue.