I've found the answer!
I'd set my Video Output in Retroarch to Vulkan, it looks like for the games to work (specifically) via Launchbox that I need to change the Video Output back to D3d12. I'd guess that when running games directly through Retroarch the video driver (this might not be the right terminology?) is adjusted to something other than Vulkan, but when using Launchbox it'll only use the one saved in the Retroarch config file?
Retroarch Video Output can be found in Settings --> Video --> Output --> Video
I'll have a look to see if there's any way to have a per core video driver (again, sorry if this is the wrong terminology) and report back here if i locate a method.