I think the ports you're referring to are the INs and OUTs of the MOTU? The sound from VLC suddenly started happening through Microsoft Sound Mapper - no idea what that is and it's not listed at all under Cnrtl/Panel > Sound, but it seems to be mapping the sound to the correct Output driver. I don't know how it got configured that way but I'm happy that it works. I haven't checked sound on the web since then but I will and I'll post back.