If you run MuvAudio.WPF.exe from the command line with the argument -? it will show you the command line options it supports.
One of the options is:
-w, --watchfolders 0 to many values accepted String A list of folders to watch for files to convert. Using this option will automatically start watching the folders with your current MuvAudio Settings.
So you can set the startup shortcut to add -w "folder path" and it should automatically start watching that folder on startup.
Let me know how this works for you and if you find any issues with the watch folder feature.
A quick question, are you able to see the "MuvAudio3" forum group? I noticed this is in MuvAudio2 and wanted to make sure MuvAudio3 was visible to all users.
Glad you're liking the new release.