No I didn't do any firmware upgrades. This is a brand new build Windows PC, I just checked my download folder, literally the only things I have downloaded and installed on it is MAME, LaunchBox, WINIPAC (but no firmware upgrade), ServoStik app (which doesn't seem to work) and JoyTray app (which does work). Initially in MAME direct I had an issue with the audio in Atari-based games (Marble Madness, Gauntlet, Super Sprint etc) having really slow audio, but that was a processor setting that I changed to fix it. I have also had to enable a few options to allow for multiple devices, like multiple trackballs and spinners and for rotary controls. But I have not touched any settings within LaunchBox/Big Box.
I tried to pause in-game and it seemed to work in the same way, so fingers crossed I'm all good now. Now that BB/LB is working I have a few questions about customising them, shall I stick them in the Noob page or non Noob ? I'm definitely a Noob !!