[Mosu]

That's intentional so that things such as adding files to a running instance via the command line (or drag & drop onto the program icon or via Windows "send to" functionality) works.

You can easily work on multiple things at the same time in that single instance, though: just open new tabs in the tool you need. Note that the job queue is run asynchronously, meaning you can continue using the tools (multiplexer, info too, chapter editor, header editor) while jobs are being executed.