Which OS are you running? For handbrake, we know that Windows XP-7 requires an active terminal where as Windows 8-10 it works even without an active terminal.
FFMPEG is a different ball game, it uses a different set of API’s which unfortunately require a user to be logged into Windows with an active terminal.
I won’t get into technical details but that’s essentially a Windows design issue as the kernel wasn’t originally designed to access hardware API’s. Microsoft has made improvements so Handbrake is able to work in kernel mode (MCEBuddy by default runs as a service in kernel mode) but FFMPEG API’s still require a logged in user with an active terminal. So if you’re using MCEBuddy and ffmpeg, ensure that a terminal is active and doesn’t log out. I believe RDP has an option to disconnect without logging out - I think that will work.
Yes but it isn’t as stable as ffmpeg so MCEBuddy doesn’t use it, but you can use it. YMMV. Let us know how it works out for you.