I'm quite new to this, but I've been able to get Launchbox running OK using Retroarch for most of the emulators I've set up so far. But, if I try and change the default emulator afgter setting a system up, the games won't start just by selecting them like normal. They are configured to be the default emulator and will run using that emulator if I choose "Launch with..." and then select the emulator, but won't start by double clicking (or via Big Box (Again, they will using "Launch with..."
For example, I set up the original Gameboy to use Retroarch, but looking at the options in Launchbox, it's not a system that' uses Retroarch, so I've set up VisualBoy Advance, which is supported, but I can only get that to work via "Launch with...." even though it's set as the default emulator.
I've got the same issue with N64 too as I decided to use Project 64 rather than Retroarch.